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Instytut Fizyki Polskiej Akademii Nauk

Division of Theoretical Physics

Institute of Physcis
Polish Academy of Sciences

Join Us

We are continuously looking for young researchers willing to join us as bachelor's or master's students, or as post-docs.
If you have any questions about these opportunities, please do not hesitate to contact one of us according to your scientific interests.

Internships

Call for pre-doctoral internships for three months at IF PAN—recruitment deadline June 25, 2024.

Masovian Symposium on Quantum, Optical and Atomic Physics (MaSQOT)

The symposium will take place in Warsaw at IF and CFT PAN from June 10 to 11, 2024. This will be an opportunity to become acquainted with the recent developments and results, exchange experiences and ideas as well as to explore new directions and initiate future collaborations among researchers working in the Masovian region.

More information about the meeting can be found on the website,

Website masqot.fuw.edu.pl

Condensed matter

Ab initio methods
Bogusławski Email ORCiD
Dynamics of growth processes
Załuska-Kotur Email Website ORCiD
Surface formation
Załuska-Kotur Email Website ORCiD
Nanowires
Buczko Email Website ORCiD Załuska-Kotur Email Website ORCiD
Polaritons
Matuszewski Email Website ORCiD
Quantum Dots
Cywiński Email Website ORCiD
Semiconductor surfaces
Buczko Email Website ORCiD Załuska-Kotur Email Website ORCiD
Topological insulators
Buczko Email Website ORCiD Matuszewski Email Website ORCiD

Ultra-cold atoms & molecules

Atomic physics with anitmatter (CERN)
Sowiński Email Website ORCiD
Bose-Einstein condensates
Gajda Email Website ORCiD Matuszewski Email Website ORCiD Deuar Email Website ORCiD Witkowska Email Website ORCiD
Degenerate fermionic matter
Gajda Email Website ORCiD Mostowski Email Website ORCiD Sowiński Email Website ORCiD
Phase space and C-field methods
Few-body problems
Sowiński Email Website ORCiD
Many-body correlations
Gajda Email Website ORCiD Sowiński Email Website ORCiD Witkowska Email Website ORCiD
Optical lattices
Gajda Email Website ORCiD Sowiński Email Website ORCiD Witkowska Email Website ORCiD
Pauli Crystals
Gajda Email Website ORCiD Mostowski Email Website ORCiD Sowiński Email Website ORCiD Załuska-Kotur Email Website ORCiD
Quantum droplets

Low-dimensional Crystalline Structures

Lead by
Ryszard Buczko Email Website ORCiD Magdalena A. Załuska-Kotur Email Website ORCiD
Research topics
Nanowires
Semiconductor surfaces
Topological insulators
Dynamics of growth processes
Surface formation
Pauli Crystals
Website

Quantum Gases Group

Lead by
Mariusz Gajda Email Website ORCiD
Research topics
Quantum simulators
Bose-Einstein condensates
Degenerate fermionic matter
Many-body correlations
Optical lattices
Pauli Crystals
Quantum droplets
Website

Polariton Group

Lead by
Michał Matuszewski Email Website ORCiD
Research topics
Polaritons
Topological insulators
Light-matter interactions
Machine learning
Quantum simulators
Bose-Einstein condensates
Website

Few Body Problems Group

Lead by
Tomasz Sowiński Email Website ORCiD
Research topics
Quantum simulators
Atomic physics with anitmatter (CERN)
Degenerate fermionic matter
Few-body problems
Many-body correlations
Optical lattices
Pauli Crystals
Website

Spin Qubit Group

Lead by
Łukasz Cywiński Email Website ORCiD
Research topics
Open quantum systems
Spin qubits
Quantum Dots
Quantum–classical transition
Website

Quantum Noise Group

Lead by
Piotr Deuar Email Website ORCiD
Research topics
Fluid dynamics
Bose-Einstein condensates
Phase space and C-field methods
Quantum droplets
Website

Biomembrans

Lead by
Bartosz Różycki Email Website ORCiD
Research topics
Biomembranes
Biomolecules
Soft matter
Website

Soft Matter and Fluids Physics Group

Lead by
Panos E. Theodorakis Email Website ORCiD
Research topics
Fluid dynamics
Soft matter
Website

Ultracold Atoms and Beyond

Lead by
Emilia Witkowska Email Website ORCiD
Research topics
Quantum metrology
Bose-Einstein condensates
Many-body correlations
Optical lattices
Website

Professors

prof. dr hab. Zofia Z. Białynicka-Birula Email ORCiD prof. dr hab. Piotr P. Bogusławski Email ORCiD prof. dr hab. Ryszard R. Buczko Email Website ORCiD prof. dr hab. Mariusz M. Gajda Email Website ORCiD prof. dr hab. Perła P. Kacman prof. dr hab. Mai M. Suan S. Li Email Website ORCiD prof. dr hab. Michał M. Matuszewski Email Website ORCiD prof. dr hab. Jan J. Mostowski Email Website ORCiD prof. dr hab. Tomasz T. Sowiński Email Website ORCiD prof. dr hab. Magdalena M. A. A. Załuska-Kotur Email Website ORCiD

Sorry, there are no upcomming seminars at this time.

June 18, 2024
prof. dr hab. Tomasz SowińskiEmail Website ORCiD
Institute of Physics, Polish Academy of Sciences
"Spectroscopy of antiprotonic atoms"

Several high-precision experiments at the Antiproton Decelerator complex at CERN aim to look for any significant differences between matter and antimatter. One of these experiments is AEḡIS, whose primary goal is to test the weak equivalence principle for antimatter by measuring (with atomic accuracy) the free fall of a neutral antihydrogen atom in the Earth's gravitational field. It turns out that the experimental setup and techniques developed at AEḡIS, when expanded appropriately, can be used to produce on-demand complex bound states of matter and antimatter, and then to study their spectroscopic properties. One such natural direction is the possibility of producing neutral antiprotonic atoms, i.e., atoms in which one of the electrons is substituted by almost 2,000 times heavier antiproton. During my talk, I will present how this research can contribute to a better understanding of the bound states of matter and antimatter, as well as the internal structure of atomic nuclei, and how it could potentially become yet another opportunity for precise testing of fundamental theories.

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May 21, 2024
dr Michał Parniak
CENT, University of Warsaw
"Rydberg atom quantum sensing"

Rydberg atoms are an established platform for quantum technologies, with new applications still emerging. Large dipole moment of Rydberg atoms allows for their well-known interacting properties, facilitating e.g. quantum gates. The same property also allows for detection of external fields, using transitions between two Rydberg states. Remarkably, these properties hold even in hot-atom vapor cell systems. I will present our results on detecting as well as transducing microwave and terahertz radiation into the optical domain. I will also discuss sensitivity limits, and show how we can achieve detection of thermal radiation, also in cryogenic conditions. I will also hint at ongoing cold-atom based experiments aimed at demonstrating ultimate quantum-metrological limits of sensing via collective qubit lifetime-extension techniques inspired by our past experiments with quantum memories. Those approaches hold a promise to realise optimal sensing protocol, towards reaching the standard quantum limit.

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May 14, 2024
dr Mircea Trif, prof. IFPAN
Institute of Physics, Polish Academy of Sciences
"Cavity magnonics with domain walls in insulating ferromagnetic wires"

Magnetic domain walls (DWs) are topological defects that exhibit robust low-energy modes that can be harnessed for classical and neuromorphic computing. However, the quantum nature of these modes has been elusive thus far. Using the language of cavity optomechanics, we show how to exploit a geometric Berry-phase interaction between the localized DWs and the extended magnons in short ferromagnetic insulating wires to efficiently cool the DW to its quantum ground state or to prepare nonclassical states exhibiting a negative Wigner function that can be extracted from the power spectrum of the emitted magnons. Moreover, we demonstrate that magnons can mediate long-range entangling interactions between qubits stored in distant DWs, which could facilitate the implementation of a universal set of quantum gates. Our proposal relies only on the intrinsic degrees of freedom of the ferromagnet, and can be naturally extended to explore the quantum dynamics of DWs in ferrimagnets and antiferromagnets, as well as quantum vortices or skyrmions confined in insulating magnetic nanodisks.

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May 7, 2024
Mr. Midhun Anila
Institute of Physics, Polish Academy of Sciences
"Multi-scale simulations of galectin-3"

Intrinsically disordered proteins (IDPs) at physiological conditions have no well-defined, stable structure in extended parts of their polypeptide chains. They participate in many processes in biological cells, including signaling, cell-cycle regulation, and initiation of translation.
IDPs are major components of biomolecular condensates (BCs) that form through liquid-liquid phase separation in biological cells. Despite considerable research on BCs in the cytosol and nucleus, their behavior at cellular membranes remains largely unexplored.
Galectin-3 is a protein comprising an intrinsically disordered N-terminal domain (NTD) and a well-folded carbohydrate recognition domain (CRD) which can bind to glycosphingolipids on the cell membrane. Galectin-3 is known to mediate clathrin-independent endocytosis [1] and has been recently shown to undergo liquid-liquid phase separation [2], but the function of the BCs of galectin-3 in the endocytic pit formation is unknown.
Using dissipative particle dynamics (DPD) simulations, we explore how polymer models resembling galectin-3 sense and respond to membrane curvature. Our findings suggest a generic mechanism by which BCs sense membrane curvature, potentially influencing such cellular processes as endocytosis [3]. To elucidate the conformational dynamics of galectin-3, we have conducted molecular dynamics simulations using the Martini 3 force field. Following the method introduced by Thomasen et al. [4] for rescaling protein-water interactions, we generate a conformational ensemble in good quantitative agreement with data from small angle X-ray scattering experiments [5]. Our simulations reveal large-scale fluctuations between compact and extended conformations of galectin-3, with aromatic residues within the NTD forming most frequent contacts [6].

[1] Lakshminarayan, R., Wunder, C., Becken, U., Howes, M. T., Benzing, C., Arumugam, & Johannes, L. (2014). Galectin-3 drives glycosphingolipid-dependent biogenesis of clathrin-independent carriers. Nature Cell Biology, 16(6), 592-603.
[2] Chiu, Y. P., Sun, Y. C., Qiu, D. C., Lin, Y. H., Chen, Y. Q., Kuo, J. C., & Huang, J. R. (2020). Liquid-liquid phase separation and extracellular multivalent interactions in the tale of galectin-3. Nature Communications, 11(1), 1229.
[3] Anila, M. M., Ghosh, R., & Różycki, B. (2023). Membrane curvature sensing by model biomolecular condensates. Soft Matter, 19(20), 3723-3732.
[4] Thomasen, F. E., Pesce, F., Roesgaard, M. A., Tesei, G., & Lindorff-Larsen, K. (2022). Improving Martini 3 for disordered and multidomain proteins. Journal of Chemical Theory and Computation, 18(4), 2033-2041.
[5] Lin, Y. H., Qiu, D. C., Chang, W. H., Yeh, Y. Q., Jeng, U. S., Liu, F. T., & Huang, J. R. (2017). The intrinsically disordered N-terminal domain of galectin-3 dynamically mediates multisite self-association of the protein through fuzzy interactions. Journal of Biological Chemistry, 292(43), 17845-17856.
[6] Anila, M. M., Rogowski P., & Różycki, B. (2024). Scrutinising the conformational ensemble of the intrinsically mixed-folded protein galectin-3. Under review.

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April 23, 2024
dr hab. Łukasz CywińskiEmail Website ORCiD
Institute of Physics, Polish Academy of Sciences
"Quantum computing with silicon quantum dots"

Classical computers are made from semiconductors, but semiconductor-based architectures for quantum computers are still less developed than those based on superconducting circuits, trapped ions, or neutral atoms. I will try to convince you that there are good reasons to still pursue the "semiconductor path" to quantum computers, and discuss challenges that need to be overcome on this path. I will also discuss what kinds of interesting physical problems from solid state physics and open quantum system physics one can grapple with, while contributing to a somewhat "engineering-like" task of building a scalable quantum computer.

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April 16, 2024
dr hab. Karol Szałowski
University of Łódź, Faculty of Physics and Applied Informatics, Department of Solid State Physics
"Tailoring proximity effects in graphene-based van der Waals heterostructures with charge density waves and magnetism in TaS2 and NbS2"

Proximity effects constitute a highly promising tool for versatile engineering of the band structure of graphene in van der Waals heterostructures [1]. Particularly promising relevant systems are based on transition metal dichalcogenides [2]. In the paper some approaches to tune the proximity effects in reversible manner will be discussed. A main one is based on charge density wave degree of freedom. Such a low-temperature ordering is known to develop in 1T polytypes of TaS2 and NbS2, enabling to manipulate the band structure of heterostructures in twistronic-like way without physical alteration of the twist angle.
In the paper the DFT calculations-based predictions of proximity effects in graphene band structure emerging in heterostructures with TaS2 [3] and NbS2 and controllable with charge density wave ordering will be presented. Moreover, magnetism in TaS2 [4] will be discussed as yet another mechanism capable of shaping the proximity effects. Also the external electric field will be demonstrated to be an additional useful factor influencing the band structure.
The interpretation of the results will be based on symmetry-based tight-binding Hamiltonians [3]. Special emphasis will be put on proximity-induced Rashba spin-orbit coupling parametrized by characteristic energy and tuneable angle (inducing possible anisotropic Rashba–Edelstein effect).

Acknowledgements: Financial support provided by the University of Łódź under Grant No. 1/IDUB/DOS/2021 is gratefully acknowledged. Polish high-performance computing infrastructure PLGrid (HPC Centers: ACK Cyfronet AGH) is gratefully acknowledged for providing computer facilities and support within computational grant no. PLG/2023/016571.

[1] J. F. Sierra, J. Fabian, R. K. Kawakami, S. Roche and S. O. Valenzuela, Nature Nanotechnology 16 (2021) 856.
[2] M. Gmitra and J. Fabian, Physical Review B 92 (2015) 155403.
[3] K. Szałowski, M. Milivojević, D. Kochan and M. Gmitra, 2D Materials 10 (2023) 025013.
[4] I. Lutsyk, K. Szałowski et al., Nano Research 16 (2023) 11528.

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April 9, 2024
dr Paweł KrupaEmail ORCiD
Institute of Physics, Polish Academy of Sciences
"Computational Studies of Environmental Effects on the Structure and Dynamics of Proteins"

The function of most proteins is strictly connected to their structure, which depends on their sequence and external factors, such as the surrounding environment. Interactions of proteins with lipid bilayers, for example, can significantly affect both systems and strongly depend on the lipid composition. This presentation will focus on demonstrating how external factors can impact protein structure and dynamics, examined through molecular dynamics simulations. I will present examples of several protein systems in bulk water, as well as when interacting or embedded into lipid bilayers of various compositions and how environmental conditions and other factors, such as the presence or absence of disulfide bonds, can influence them.

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March 26, 2024
dr Karol Gietka
Institut für Theoretische Physik, Universität Innsbruck
"Singular quantum Fisher information matrix in critical metrology"

Critical metrology relies on the extreme sensitivity of the system's eigenstates close to the critical point to Hamiltonian parameter perturbations. Typically, however, the critical point, at which the phase transition occurs, is a function of many if not all the parameters of the system. This suggests that the quantum Fisher information matrix might be singular at the critical point, which in the context of parameter estimation is typically representing a significant complication. On the example of a toy-model Landau-Zener Hamiltonian, the Ising Hamiltonian, and the thermodynamic limit of the Lipkin-Meshkov-Glick Hamiltonian, we show that the quantum Fisher information matrix in critical metrology is always singular regardless of the system size and the distance to the critical point. However, contrary to the regular approach to metrology, where the singularity is detrimental, we argue that critical metrology works precisely because the quantum Fisher information matrix is singular.

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March 19, 2024
prof. dr hab. Piotr Szymczak
Faculty of Physics, University of Warsaw
"On the Ideal Shapes of Stalagmites"

Stalagmites are column-like formations that rise from the floor of caves. They are formed by the buildup of minerals deposited from water dripping from the ceiling. The water dissolves minerals, such as calcium carbonate, from the rock above. As the water drips down, it loses carbon dioxide to the cave air. This causes the minerals to come out of solution and precipitate onto the cave floor, slowly building up the stalagmite.

Nearly sixty years ago, Franke formulated a mathematical model for the growth of stalagmites. In this model, the local growth rate of a stalagmite is proportional to the oversaturation of calcium ions in the solution dripping down the stalagmite's surface. Franke postulated that - provided the physical conditions in the cave remain constant - after a sufficiently long period, the stalagmite will assume an ideal shape, which in later stages of growth will only move upwards without further change in its form. These conclusions were later confirmed in computer simulations yet the mathematical form of this ideal shape was not discovered.

As we will show, Franke's model for stalagmite growth can be solved analytically, finding invariant, Platonic forms of stalagmites that could be observed in an "ideal cave", under constant physical conditions and with a constant flow of water dripping from an associated stalactite. Interestingly, it turns out that the shape numerically found in previous numerical studies is just one of a whole family of solutions. These new solutions describe stalagmites with a flat area at their peak of a certain fixed diameter, and conical stalagmites, with sharply pointed tops. All of these forms are observed in caves.

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March 12, 2024
dr Helgi Sigurðsson
Faculty of Physics, University of Warsaw & Science Institute, University of Iceland
"Interacting Networks of Liquid Light"

Recent years have seen a surge of advancements in optical manipulation over bosonic light-matter quasiparticles known as exciton-polaritons in semiconductor microcavities. These particles appear under strong-coupling conditions between confined cavity photons and embedded quantum-well excitons. Characterised by very high interaction strengths, nonlinearities, and picosecond timescales, they provide an exciting testbed to explore room-temperature nonequilibrium Bose-Einstein condensation in the optical regime.

In this talk, I will present results on all-optically engineered macroscopic networks of connected exciton-polariton condensates, which permit studies on fundamental emergent behaviours in nonequilibrium quantum fluidic systems that are subject to an external drive and dissipation. I will explain how pumped polariton fluids give rise to so-called “ballistic condensates” which can interfere to form a bosonic analog of time-delay coupled oscillations, a behavior found all across nature. I will present experimental and theoretical results on large-scale condensate networks displaying aforementioned emergent behaviors, including: spontaneous synchronization with unprecedented long-range spatial and temporal correlations [1,2], formation of persistent circulating mass currents [3], non-invasive optical control of the network coupling weights [4], synthesis of artificial lattices for studies of non-Hermitian topological physics and Bloch band formation [5,6], and vortex frustration [7].

Lastly, I will discuss recent developments on the role of polariton condensate networks as nonlinear information processing elements in the optical computing paradigm. I will address three examples: room-temperature optical logic, analog spin simulators, and as neuromorphic computing hardware.

[1] Töpfer et al., Communication Physics 3, 2 (2020).
[2] Töpfer et al., Optica 8, 106 (2021).
[3] Cookson et al., Nature Communications 12, 2120 (2021).
[4] Alyatkin et al., Physical Review Letters 124, 207402 (2020).
[5] Pickup et al., Nature Communications 11, 4431 (2020).
[6] Alyatkin et al., Nature Communications 12, 5571 (2021).
[7] Alyatkin et al., arXiv:2207.01850 (2022).

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March 5, 2024
prof. Zbigniew R. Struzik
University of Tokyo
"On the dynamics of progress"

Autonomy is a unique defining feature of living systems, from bacteria -- or even from viruses, the organisms at the 'edge of life' -- striving to survive in evolving environment. Yet, evolution is a collective phenomenon requiring interaction, 'counterintuitively' to autonomic thinking of individual organisms allowing their species to survive.
Such an apparent dichotomy and the struggle of the 'opposites' is ubiquitous in most complex dynamical systems, entailing complex adaptive systems which encompass living systems. The struggle of the opposites underlies most if not all roads to progress, understood as the evolution of 'fitness' -- be it adaptation to environment for species survival or evolution of scientific paradigms, or indeed, the evolution of the market share for those financially challenged.

Curiously, the concept of the 'roads to progress' has to date not sufficiently been studied using the language of physics of complexity. Indeed, physics traditionally understood, stayed away from investigating phenomena involving engaging in any laws of -- and due to -- individual and individualised behaviour. Yet, as becomes apparent, such seemingly impenetrable problems as evolution of social standards such as morality or religion are not principally different from evolution of scientific paradigms and innovation, these in turn not being that different from the evolution of generic actors in a competitive company market.

Such universality is where physics can flourish and indeed, a rapidly growing range of reports shows intriguing beauty of the phenomena characterising the dynamics of the road to progress. In my talk, I will present our own recent work on the game-of-life like system which - to our surprise - showed exciting richness of critical phenomena. I will also refer to selected works in order to encourage listeners to engage in research of the 'physics of struggle'.

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February 20, 2024
dr Amir RahmaniEmail ORCiD
Institute of Physics PAS
"Non-Hermitian physics and phase transitions"

A physical system may become non-conservative when it is interacting with its environment. One way to introduce openness is by breaking the Hermiticity, that is, by involving non-Hermitian matrices/operators. This seminar will provide a quick overview of the theoretical background of non-Hermitian physics, followed by a focus on the topic of non-Hermitian phase transitions intertwined with the physics of light-matter interactions.

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February 13, 2024
prof. Gediminas Juzeliūnas
Institute of Theoretical Physics and Astronomy, Vilnius University, Vilnius, Lithuania
"Spin Squeezing for Ultracold Fermions in Optical Lattices"

In the initial part of the talk an extended overview will be presented on individual and collective spins, the states of the collective spin, squeezing the collective spin states. We will also talk about different spin squeezing mechanisms including one axis twisting (OAT), and two axis countertwisting (TACT) spin squeezing models. Subsequently we will discuss possibilities to produce spin squeezing for spinful atomic fermions in optical lattices. It is shown that by applying laser radiation one can simulate not only OAT but also TACT spin squeezing models, the latter TACT model providing better squeezing. The spin squeezing generated in this way is mediated by spin waves playing a role of the intermediate states facilitating the squeezing process. The spin squeezing can be used for increasing sensitivity of atomic clocks.

More about this work:
Phys. Rev. Lett. 129, 090403 (2022)
Phys. Rev. B 108, 104301 (2023)

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P. D. Lan, D. A. Nissley, E. P. O’Brien, T. T. Nguyen, M. S. LiEmail Website ORCiD
Deciphering the free energy landscapes of SARS-CoV-2 wild type and Omicron variant interacting with human ACE2
The Journal of Chemical Physics, 160, 055101 (2024)
#11 Number of Publications
I. Białynicki-Birula, Z. Białynicka-BirulaEmail ORCiD, S. Augustynowicz
Reply to comments on 'Backflow in relativistic wave equations'
J. Phys. A: Math. Theor., 56, 138001 (2023)
T. Zeng, B. Liu, L. Bi, et al, incl. P. E. TheodorakisEmail Website ORCiD
Effects of different drying methods on quality and water distribution of Lycium barbarum
J. Food Process Eng., 46(12), e14482 (2023)
M. B. KrukEmail ORCiD, T. Vibel, J. Artl, P. Kulik, K. Pawłowski, K. Rzążewski
Fock State Sampling Method — Characteristic Temperature of Maximal Fluctuations for Interacting Bosons in Box Potentials
Acta Phys. Pol. A, 6(143), 171 (2023)
A. Eisenreichova , M. Klima , M. M. Anila, et al, incl. B. RóżyckiEmail Website ORCiD
Crystal Structure of the ORP8 Lipid Transport ORD Domain: Model of Lipid Transport
Cells, 12(15), 1974 (2023)
Hoang Linh Nguyen, Nguyen Quoc Thai, Mai Suan LiEmail Website ORCiD
Identifying inhibitors of NSP16-NSP10 of SARS-CoV-2 from large databases
Journal of Biomolecular Structure and Dynamics, 41(15), 7045 (2023)
P. R. Pandey, B. RóżyckiEmail Website ORCiD, T. R. Weikl
Molecular Dynamics Simulations of Immune Receptors and Ligands
The Immune Synapse Methods and Protocols, Methods in Molecular Biology, 2654, 51 (2023)
Xiaofang Shan, Bin Liu, Zongsheng Zhu, Rachid Bennacer, Rounan Wang, Panagiotis E. TheodorakisEmail Website ORCiD
Analysis of the heat transfer in electronic radiator filled with metal foam
Energies, 16, 4224 (2023)
Liu Bin, Hu Hengxiang, Bi Lisen, Panagiotis E. TheodorakisEmail Website ORCiD, Zeng Tao
Effect of the arrangement of two nozzles on morphology, velocity, and particle size distribution of artificial snow-making spray field
Physics of Fluids, 35, 052236 (2023)
Reinhard Lipowsky, Rikhia Ghosh, Vahid Satarifard, et al, incl. Bartosz RóżyckiEmail Website ORCiD
Leaflet Tensions Control the Spatio-Temporal Remodeling of Lipid Bilayers and Nanovesicles
Biomolecules, 13(6), 926 (2023)
Vu V. Q., Nissley D. A., Jiang Y., O’Brien E. P., Li M. S.Email Website ORCiD
Is Posttranslational Folding More Efficient Than Refolding from a Denatured State: A Computational Study
J. Phys. Chem. B, 127 (21), 4761 (2023)
Gabovich A. M., Voitenko A. I., Ekino T., et al, incl. Li M. S.Email Website ORCiD
Coexistence of superconductivity and charge-density waves: evidence from tunneling studies
Low Temperature Physics, 49(7), 881 (2023)
N. Karska, I. Zhukov, A. D. Lipińska, S. Rodziewicz-Motowidło, P. KrupaEmail ORCiD
Why does the herpes simplex 1 virus-encoded UL49.5 protein fail to inhibit the TAP-dependent antigen presentation?
BBA-Biomembranes, 1865(8), 184200 (2023)
M. Graul, N. Karska, M. Wąchalska, et al, incl. P. KrupaEmail ORCiD
The N-terminal Proline Hinge Motif Controls the Structure of Bovine Herpesvirus 1-encoded Inhibitor of the Transporter Associated with Antigen Processing Required for its Immunomodulatory Function
Journal of Molecular Biology, 435, 167964 (2023)
L. Bi, B. Liu, Z. Zhu, P. E. TheodorakisEmail Website ORCiD, H. Hu,  Z. Li 
Molecular dynamics simulation of Wenzel-state nanodroplets: Evaporation on heated substrates with different rough structures
Physics of Fluids, 35, 012015 (2023)
B. Liu, Z. Li, L. Bi, et al, incl. P. E. TheodorakisEmail Website ORCiD
Characteristics of HFE7100 droplets evaporation on substrates with different thermal conductivity
Thermal Science and Engineering Progress, 40, 101771 (2023)
#57 Number of Publications
A. Chen, H. Zhang, J. Song, B. Liu, C. Zhang, P. E. TheodorakisEmail Website ORCiD
On the meniscus shape and marangoni flow in capillary tubes with noncircular cross-section shapes
Eur. Phys. J. Appl. Phys. , 97, 77 (2022)
N. H. Linh, V. H. Man, M. S. LiEmail Website ORCiD, et al
Molecular dynamics simulation of cancer cell membrane perforated by shockwave induced bubble collapse
J. Chem. Phys., 157, 225102 (2022)
B.A. Orlowski , K. Gwozdz, K. Goscinski, et al
Extended Defect States in CdTe/ZnTe Photojunction
Acta Phys. Pol. , 5, 548 (2022)
L. Glöggler, R. Caravita, M. Auzins, et al, incl. T. SowińskiEmail Website ORCiD
High-resolution MCP-TimePix3 imaging/timing detector for antimatter physics
Meas. Sci. Technol., 33, 115105 (2022)
H. Nguyen, M. S. LiEmail Website ORCiD
Antibody–nanobody combination increases their neutralizing activity against SARS-CoV-2 and nanobody H11-H4 is effective against Alpha, Kappa and Delta variants
Scientific Reports, 12, 9701 (2022)
H. L. Nguyen, N. Q. Thai, P. H. Nguyen, M. S. LiEmail Website ORCiD
SARS-CoV-2 Omicron Variant Binds to Human Cells More Strongly than the Wild Type: Evidence from Molecular Dynamics Simulation
J. Phys. Chem. B, 126, 4669 (2022)
H. L. Nguyen, N. Q. Thai, M. S. LiEmail Website ORCiD
Determination of Multidirectional Pathways for Ligand Release from the Receptor: A New Approach Based on Differential Evolution
J. Chem. Theory Comput., 18, 3860 (2022)
B. RóżyckiEmail Website ORCiD, E. Boura
Conformational ensemble of the full-length SARS-CoV-2 nucleocapsid (N) protein based on molecular simulations and SAXS data
Biophysical Chemistry, 288, 106843 (2022)
J. Dorival, S. Moraïs, A. Labourel, et al
Mapping the deformability of natural and designed cellulosomes in solution
Biotechnology for Biofuels and Bioproducts, 15, 68 (2022)
B. Liu, S. Shi, H. Yin, P. E. TheodorakisEmail Website ORCiD, R. Bennacer
COMPARATIVE EXPERIMENTAL STUDY ON MICROCHANNEL AND FINNED-TUBE EVAPORATORS IN A WINDOW AIR-CONDITIONING SYSTEM
Journal of Enhanced Heat Transfer, 29, 51 (2022)
H. L. Nguyen, H. Q. Linh, P. KrupaEmail ORCiD, G. La Penna, M. S. LiEmail Website ORCiD
Amyloid β Dodecamer Disrupts the Neuronal Membrane More Strongly than the Mature Fibril: Understanding the Role of Oligomers in Neurotoxicity
J. Phys. Chem. B , 126, 3659 (2022)
P. Szulim, M. Trippenbach, Y. B. Band, M. GajdaEmail Website ORCiD, M. Brewczyk
Atoms in a spin dependent optical potential: ground state topology and magnetization
New J. Phys., 24, 033041 (2022)
H. L. Nguyen, V. H. Man, M. S. LiEmail Website ORCiD, P. Derreumaux, J. Wang,  P. H. Nguyen
Elastic moduli of normal and cancer cell membranes revealed by molecular dynamics simulations
Phys. Chem. Chem. Phys., 24, 6225 (2022)
H. Nguyen, P. D. Lan, D. A. Nissley, E. P. O’Brien, M. S. LiEmail Website ORCiD
Cocktail of REGN Antibodies Binds More Strongly to SARS-CoV-2 Than Its Components, but the Omicron Variant Reduces Its Neutralizing Ability
J. Phys. Chem. B, 126, 2812 (2022)
B. Liu, J. Li, A. Chen, P. E. TheodorakisEmail Website ORCiD, Z. Zhu, J. Yu
Selection of the cold logistics model based on the carbon footprint of fruits and vegetables in China
Journal of Cleaner Production, 334, 130251 (2022)
B. Liu, S. Shi, Y. Liu, R. Bennacer, A. Chen, P. E. TheodorakisEmail Website ORCiD
Effect of Different Plenum-Chamber Coefficients on the Frosting of Air-Cooler
Energies, 15, 422 (2022)
A. Liwo, A. K. Sieradzan, A. S. Karczyńska, et al, incl. P. KrupaEmail ORCiD
Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry
Practical Aspects of Computational Chemistry, V, 31 (2022)
#49 Number of Publications
P. Comaron, I. Carusotto, M. H. Szymańska, N. P. Proukakis
Non-equilibrium Berezinskii-Kosterlitz-Thouless transition in driven-dissipative condensates
Europhysics Letters , 133, 17002 (2021)
S. E. Leininger, J. Rodriguez, Q. V. Vu, et al, incl. M. S. LiEmail Website ORCiD
Ribosome Elongation Kinetics of Consecutively Charged Residues Are Coupled to Electrostatic Force
Biochemistry, 60, 3223 (2021)
A. K. Sieradzan, C. Czaplewski, P. KrupaEmail ORCiD, et al
Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
Protein Folding, Methods in Molecular Biology , 2376, 399 (2021)
A. Antoniak, I. Biskupek, K.  K.Bojarski, et al, incl. P. KrupaEmail ORCiD
Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
Journal of Molecular Graphics and Modelling , 108, 108008 (2021)
M. Król, K. Rechcińska, H. Sigurdsson, et al, incl. M. MatuszewskiEmail Website ORCiD
Realizing Optical Persistent Spin Helix and Stern-Gerlach Deflection in an Anisotropic Liquid Crystal Microcavity
Physical Review Letters , 127, 190401 (2021)
B. Liu, S. Shi, Y. Liu, R. Bennacer, A. Chen, P. E. TheodorakisEmail Website ORCiD
Study on the effect of different plenum chamber coefficients on frosting of air-cooler
E3S Web Conferences, 321, 04019 (2021)
A. M. Vera, A. Galera-Prat, M. Wojciechowski, et al, incl. B. RóżyckiEmail Website ORCiD
Cohesin-dockerin code in cellulosomal dual binding modes and its allosteric regulation by proline isomerization
Structure, 29, 587 (2021)
Q. V. Vu, Y. Jiang, M. S. LiEmail Website ORCiD, E. P. O'Brien
The Driving Force for Co-translational Protein Folding is Weaker In the Ribosome Vestibule due to Greater Water Ordering
Chemical Science , 12, 11851 (2021)
A. Eisenreichova, B. RóżyckiEmail Website ORCiD, E. Boura, J. Humpolickova
Osh6 Revisited: Control of PS Transport by the Concerted Actions of PI4P and Sac1 Phosphatase
Frontiers in Molecular Bioscience, 8, 747601 (2021)
P. R. Pandey, B. RóżyckiEmail Website ORCiD, R. Lipowsky, T. R. Weikl
Structural variability and concerted motions of the T cell receptor – CD3 complex
eLife, 10, e67195 (2021)
M. Załuska-KoturEmail Website ORCiD, H. Popova, V. Tonchev
Step Bunches, Nanowires and Other Vicinal "Creatures"—Ehrlich–Schwoebel Effect by Cellular Automata
Crystals, 11, 1135 (2021)
V. H. Man, M. S. LiEmail Website ORCiD, P. Derreumaux, J. Wang, P. H. Nguyen
Molecular Mechanism of Ultrasound-Induced Structural Defects in Liposomes: A Nonequilibrium Molecular Dynamics Simulation Study
Langmuir, 37, 7945 (2021)
H. Nguyen, P. D. Lan, D. A. Nissley, E. P. O’Brien, M. S. LiEmail Website ORCiD
Electrostatic Interactions Explain the Higher Binding Affinity of the CR3022 Antibody for SARS-CoV-2 than the 4A8 Antibody
J. Phys. Chem. B, 125, 7368 (2021)
A. B. Poma, T. T. M. Thu, L. T. M. Tri, H. L. Nguyen, M. S. LiEmail Website ORCiD
Nanomechanical Stability of Aβ Tetramers and Fibril-like Structures: Molecular Dynamics Simulations
J. Phys. Chem. B, 125, 7628 (2021)
R. Szymko, M. Denys, T. Bulik, et al
Application of Spatio-Temporal Spectral Analysis for Detection of SeismicWaves in Gravitational-Wave Interferometer
Galaxies, 9, 50 (2021)
P. KrupaEmail ORCiD, A. S. Karczyńska, M. A. Mozolewska, A. Liwo, C. Czaplewski
UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations
Bioinformatics , 37, 1613 (2021)
P. KrupaEmail ORCiD, M. Spodzieja, A. K.Sieradzan
Prediction of CD28-CD86 protein complex structure using different level of resolution approach
Journal of Molecular Graphics and Modelling, 103, 107802 (2021)
D. Marasco, C. Vicidomini, P. KrupaEmail ORCiD, et al, incl. M. S. LiEmail Website ORCiD
Plant isoquinoline alkaloids as potential neurodrugs: A comparative study of the effects of benzo[c]phenanthridine and berberine-based compounds on β-amyloid aggregation
Chemico-Biological Interactions, 334, 109300 (2021)
P. E. TheodorakisEmail Website ORCiD, Y. Wang, A. Chen, B. Liu
Off-lattice Monte-Carlo approach for studying nucleation and evaporation phenomena at the molecular scale
Materials, 14, 2092 (2021)
B. RóżyckiEmail Website ORCiD, T. R. Weikl 
Cooperative stabilization of close-contact zones leads to sensitivity and selectivity in T-cell recognition
Cells, 10, 1023 (2021)
R. Rechciński, M. Galicka, M. Simma, et al, incl. P. Kacman, R. BuczkoEmail Website ORCiD
Structure Inversion Asymmetry and Rashba Effect in Quantum Confined Topological Crystalline Insulator Heterostructures
Adv. Funct. Mater., 31, 2008885 (2021)
M. Banchelli, R. Cascella, C. D’Andrea, et al, incl. M. S. LiEmail Website ORCiD
Probing the Structure of Toxic Amyloid-β Oligomers with Electron Spin Resonance and Molecular Modeling
ACS Chemical Neuroscience, 12, 1150 (2021)
L. Li, J. Hu, X. Shi, B. RóżyckiEmail Website ORCiD, F. Song
Interplay between cooperativity of intercellular receptor-ligand binding and coalescence of nanoscale lipid clusters in adhering membranes
Soft Matter, 17, 1912 (2021)
K. Brown, T. Bland, P. Comaron, N. P. Proukakis
Periodic quenches across the Berezinskii-Kosterlitz-Thouless phase transition
Phys. Rev. Research, 3, 013097 (2021)
P. H. Nguyen, A. Ramamoorthy, B. R. Sahoo, et al, incl. M. S. LiEmail Website ORCiD
Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer’s Disease, Parkinson’s Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis
Chem. Rev., 121, 2545 (2021)
A. Sicorello, B. RóżyckiEmail Website ORCiD, P. V. Konarev, D. I. Svergun, A. Pastore
Capturing the conformational ensemble of the mixed folded polyglutamine protein ataxin-3
Structure, 29, 70 (2021)
#61 Number of Publications
A. S. Karczynska, K. Zieba, U. Uciechowska, et al, incl. P. KrupaEmail ORCiD
Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13
Journal of Chemical Information and Modeling, 60, 1844 (2020)
A. Liwo, C. Czaplewski, A. K. Sieradzan, et al, incl. P. KrupaEmail ORCiD
Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers
Progress in Molecular Biology and Translational Science, 170, 73 (2020)
D. A. Nissley, Q. V. Vu, F. Trovato, et al, incl. M. S. LiEmail Website ORCiD
Electrostatic Interactions Govern Extreme Nascent Protein Ejection Times from Ribosomes and Can Delay Ribosome Recycling
Journal of the American Chemical Society, 142, 6103 (2020)
D. Q. H. Pham, P. KrupaEmail ORCiD, H. L. Nguyen, G. L. Penna, M. S. LiEmail Website ORCiD
Computational Model to Unravel the Function of Amyloid-βPeptides in Contact with a Phospholipid membrane
The Journal of Physical Chemistry B, 124, 3300 (2020)
H. L. Nguyen, T. Q. Nguyen, D, T. Truong, M. S. LiEmail Website ORCiD
Remdesivir Strongly Binds to both RNA-dependent RNA Polymerase and Main Protease of SARS-CoV-2: Evidence from Molecular Simulations
The Journal of Physical Chemistry B, 124, 11337 (2020)
H. L. Nguyen, L. D. Pham, T. Q. Nguyen, D. A. Nissley, E. P. O’Brien, M. S. LiEmail Website ORCiD
Does SARS-CoV-2 Bind to Human ACE2 More Strongly Than Does SARS-CoV?
The Journal of Physical Chemistry B, 124, 7336 (2020)
H. L. Nguyen, H. Q. Linh, P. Matteini, G. L. Penna, M. S. LiEmail Website ORCiD
Emergence of Barrel Motif in Amyloid-β Trimer: A Computational Study
The Journal of Physical Chemistry B , 124, 10617 (2020)
A. M. Gabovich, M. S. LiEmail Website ORCiD, H. Szymczak, A. I. Voitenko 
Electric dipole image forces in three-layersystems: The classical electrostatic model
The Journal of Chemical Physics, 152, 094705 (2020)
T. C. Nguyen, L. D. Pham, D. Q. H. Pham, M. S. LiEmail Website ORCiD
Heat-induced degradation of fibrils: Exponential vs logistic kinetics
The Journal of Chemical Physics, 152, 115101 (2020)
M. Gancar, K. Ho, Sk. A. Mohid, et al, incl. M. S. LiEmail Website ORCiD
7 Methoxytacrine and 2 Aminobenzothiazole Heterodimers: Structure−Mechanism Relationship of Amyloid Inhibitors Based on Rational Design
ACS Chemical Neuroscience, 11, 715 (2020)
T. Q. Nguyen, P. E. TheodorakisEmail Website ORCiD, M. S. Li 
Fast estimation of the blood-brain barrier permeability by pulling a ligand through a lipid membrane
Journal of Chemical Information and Modeling, 60, 3057 (2020)
S. Boopathi,  D. Q. H. Pham,  W. Gonzalez, P. E. TheodorakisEmail Website ORCiD, M. S. LiEmail Website ORCiD
Zinc binding promotes greater hydrophobicity in Alzheimer’s Ab42 peptide than copper binding: Molecular dynamics and solvation thermodynamics studies
Proteins: Structure, function and bioinformatics, 88, 1285 (2020)
M. Banchelli, R. Cascella, C. D'Andrea, et al, incl. M. S. LiEmail Website ORCiD
Nanoscopic insights into the surface conformation of neurotoxic amyloid β oligomers
The Royal Society of Chemistry Advances, 10, 21907 (2020)
H. L. Nguyen, L. D. Pham, T. Q. Nguyen, D. A. Nissley, E. P. O’Brien, M. S. LiEmail Website ORCiD
Does SARS-CoV 2 Bind to Human ACE2 More Strongly Than Does SARS-CoV?
The Journal of Physical Chemistry B, 124, 7336 (2020)
V. M. Hoang, M. S. LiEmail Website ORCiD, P. Derreumaux, et al
Molecular mechanism of ultrasound interaction with a blood brain barrier model
The Journal of Chemical Physics, 153, 045104 (2020)
T. Ekino, A. M. Gabovich, M. S. LiEmail Website ORCiD, H. Szymczak, A. I. Voitenko 
Break-junction tunneling spectra of Bi2212 superconducting ceramics: Influence of inhomogeneous d-wave-Cooper-pairing and charge-density-wave order parameters
Low Temperature Physics, 46, 400 (2020)
B. Liu, S.W. Wang, L. Chai, G. El Achkar, A. Chen, P. E. TheodorakisEmail Website ORCiD
Experimental investigation of nanoparticles distribution mechanisms and deposition patterns during nanofluid droplet evaporation
Eur. Phys. J. Appl. Phys., 92, 11101 (2020)
A. Zamora, G. Dagvadorj, P. Comaron, I. Carusotto, N. P. Proukakis, M. H. Szymańska
Kibble-Zurek Mechanism in Driven Dissipative Systems Crossing a Nonequilibrium Phase Transition
Phys. Rev. Lett., 125, 095301 (2020)
V. Shahnazaryan, V. K. Kozin, I. A. Shelykh, I. V. Iorsh, and O. Kyriienko
Tunable optical nonlinearity for transition metal dichalcogenide polaritons dressed by a Fermi sea
Phys. Rev. B, 102, 115310 (2020)
R. Jakieła, M. Galicka, P. Dziawa, G. Springholz, A. Barcz
SIMS accurate determination of matrix composition of topological crystalline insulator material Pb1-xSnxSe
Surface and Interface Analysis, 52, 71 (2020)
T. Bland, Q. Marolleau, P. Comaron, B. A. Malomed, N. P. Proukakis
Persistent current formation in double-ring geometries
J. Phys. B: Al. Mol. Opt. Phys., 52, 115301 (2020)
H. Popova, F. Krzyżewski, M. A. Załuska-KoturEmail Website ORCiD, V. Tonchev
Quantifying the Effect of Step−Step Exclusion on Dynamically Unstable Vicinal Surfaces: Step Bunching without Macrostep Formation
Crystal Growth & Design, 20, 7246 (2020)
M. Strzałka, D. Kwiatkowski, Ł. CywińskiEmail Website ORCiD, K. Roszak
Qubit-environment negativity versus fidelity of conditional environmental states for a nitrogen-vacancy-center spin qubit interacting with a nuclear environment
Phys. Rev. A, 102, 042602 (2020)
#62 Number of Publications