A5014387498- Material Dynamics and Properties
- Theoretical and Computational Physics
- Phase Equilibria and Thermodynamics
- nanoparticles nucleation surface interactions
- Advanced Thermodynamics and Statistical Mechanics
- Force Microscopy Techniques and Applications
- Magnetic properties of thin films
- Protein Structure and Dynamics
- Rheology and Fluid Dynamics Studies
- Micro and Nano Robotics
- Pickering emulsions and particle stabilization
- Biochemical and Structural Characterization
- Geometric and Algebraic Topology
- Block Copolymer Self-Assembly
- Nanopore and Nanochannel Transport Studies
- Genomics and Chromatin Dynamics
- Bacteriophages and microbial interactions
- Spectroscopy and Quantum Chemical Studies
- Characterization and Applications of Magnetic Nanoparticles
- RNA and protein synthesis mechanisms
- Surfactants and Colloidal Systems
- Electrostatics and Colloid Interactions
- Thermodynamic properties of mixtures
- Ubiquitin and proteasome pathways
- Polymer crystallization and properties
Johannes Gutenberg University Mainz
2016-2025
Czech Academy of Sciences, Institute of Physics
2009-2025
University of Southern Denmark
2024
University of Trento
2024
University of Applied Sciences Mainz
2018-2021
University of Lausanne
2012
Polymer Institute of the Slovak Academy of Sciences
2012
Slovak Academy of Sciences
2012
Institute of Macromolecular Compounds
2009
Massachusetts Institute of Technology
2004-2008
Our investigation of knotted structures in the Protein Data Bank reveals most complicated knot discovered to date. We suggest that occurrence this a human ubiquitin hydrolase might be related role enzyme protein degradation. While knots are usually preserved among homologues, we also identify an exception transcarbamylase. This allows us exemplify function proteins and how they may have been created.
The last years have witnessed remarkable advances in our understanding of the emergence and consequences topological constraints biological soft matter. Examples are abundant relation to (bio)polymeric systems range from characterization knots single polymers proteins that whole chromosomes polymer melts. At same time, considerable been made description interplay between physical properties complex fluids, with development techniques now allow researchers control formation interaction...
We consider an implementation of umbrella sampling in which the pertinent range states is subdivided into small windows that are sampled consecutively and linked together. This allows us to simulate without a weight function or extrapolate results neighboring window order estimate function. Additionally, we present detailed error analysis demonstrate controlled and, absence difficulties, independent sizes. In this case, efficiency our comparable multicanonical simulation with very good...
As a rule, mean-field theories applied to fluid that can undergo transition from saturated vapor at density ρυ liquid ρℓ yield van der Waals loop. For example, isotherms of the chemical potential μ(T,ρ) as function ρ fixed temperature T less than critical Tc exhibit maximum and minimum. Metastable unstable parts loop be eliminated by Maxwell construction. Van loops corresponding double minimum potentials are artifacts. Simulations μ=μcoex for ρυ<ρ<ρℓ loop, but sufficiently...
We study the excess free energy due to phase coexistence of fluids by Monte Carlo simulations using successive umbrella sampling in finite LxLxL boxes with periodic boundary conditions. Both vapor-liquid a simple Lennard-Jones fluid and between A-rich B-rich phases symmetric binary (AB) mixture are studied, varying density rho or relative concentration x_A A mixture, respectively. The character changes from spherical droplet (or bubble) minority (near curve) cylindrical finally (in center...
Protein knots, mostly regarded as intriguing oddities, are gradually being recognized significant structural motifs. Seven distinctly knotted folds have already been identified. It is by and large unclear how these exceptional structures actually fold, only recently, experiments simulations begun to shed some light on this issue. In checking the new protein submitted Data Bank, we encountered most complex smallest knots date: A recently uncovered α-haloacid dehalogenase structure contains a...
When a fluid at constant density $\ensuremath{\rho}$ in between the densities of coexisting vapor $({\ensuremath{\rho}}_{\text{v}})$ and liquid $({\ensuremath{\rho}}_{\ensuremath{\ell}})$ temperatures below criticality is studied (cubic) box finite linear dimension $L$, phase separation occurs this volume, provided $L$ large enough. For range densities, one can observe droplet (at ${\ensuremath{\rho}}_{\ensuremath{\ell}}^{\ensuremath{'}}$ slightly exceeding...
We study active Brownian particles as a paradigm for genuine nonequilibrium phase transition requiring steady driving. Access to the critical point in computer simulations is obstructed by fact that density conserved. propose method based on arguments from finite-size scaling determine points and successfully test it two-dimensional (2D) Ising model. Using this allows us accurately of at ${\mathrm{Pe}}_{\text{cr}}=40(2), {\ensuremath{\phi}}_{\text{cr}}=0.597(3)$. Based estimate, we...
In many colloidal suspensions, the micrometer-sized particles behave like hard spheres, but when non-adsorbing polymers are added to solution a depletion attraction (of entropic origin) is created. Since 60 years Asakura-Oosawa model, which simply describes as ideal soft an archetypical description for statistical thermodynamics of such systems, accounting features real colloid-polymer mixtures very well. While fugacity (which controls their concentration in solution) plays role inverse...
A key issue for skyrmion dynamics and devices are pinning effects present in real systems. While posing a challenge the realization of conventional skyrmionics devices, exploiting can enable non-conventional computing approaches if details samples quantified understood. We demonstrate that using thermal dynamics, we characterize sample ascertain spatially resolved energy landscape. To understand mechanism pinning, probe strong size shape dependence pinning. Magnetic microscopy imaging...
We examine the statistics of knots with numerical simulations a simplified model polyethylene. can simulate polymers up to 1000 monomers (each representing roughly three CH(2) groups), at range temperatures spanning coil (good solvent) and globule (bad phases. quantify abundance in phase confined polymers, their rarity swollen phase. Since our are open, we consider (and test) various operational definitions for knots, which rigorously defined only closed chains. also associate typical size...
The condensation of a supersaturated vapor enclosed in finite system is considered. A phenomenological analysis reveals that the found to be stable at densities well above coexistence. size which condenses into droplet governed by typical length scale depends on coexistence densities, temperature and surface tension. When fluctuations are neglected, chemical potential seen show discontinuity an effective spinodal point, where inhomogeneous state becomes more than homogeneous state. If taken...
Flat walls facilitate the condensation of a supersaturated vapor: classical theory heterogeneous nucleation predicts that free energy barrier DeltaF(het)*, which needs to be overcome for formation sphere-cap-shaped seeds, is smaller than DeltaF(hom)* spherical droplets in bulk by factor 0 < f(theta) 1, only depends on contact angle theta. In this Letter, we compute both and DeltaF(het)* from Monte Carlo simulations test lattice gas model (for theta can readily controlled). Even though based...
A molecular dynamics computer simulation of a glass-forming Yukawa mixture is used to study the anisotropic single particle pulled by constant force. Beyond linear response, scaling regime found where force-temperature superposition principle Peclet number holds. In latter regime, diffusion perpendicular force can be mapped on equilibrium in terms an effective temperature, whereas parallel superdiffusive behavior seen long-time limit. This associated with hopping motion from cage and...
A recently proposed method to obtain the surface free energy σ(R) of spherical droplets and bubbles fluids, using a thermodynamic analysis two-phase coexistence in finite boxes at fixed total density, is reconsidered extended. Building on comprehensive review basic theory, it shown that from this one can extract both equimolar radius Re as well Rs tension. Hence barrier needs be overcome nucleation events where critical are formed reliably estimated for range radii physical interest. It...
The computation of interfacial free energies between coexisting phases (e.g.~saturated vapor and liquid) by computer simulation methods is still a challenging problem due to the difficulty an atomistic identification interface, fluctuations on all length scales. approach estimate tension from energy excess system with interfaces relative corresponding single-phase systems does not suffer first but suffers latter. Considering $d$-dimensional area $L^{d-1}$ linear dimension $L_z$ in direction...
The computer artificial intelligence system AlphaFold has recently predicted previously unknown three-dimensional structures of thousands proteins. Focusing on the subset with high-confidence scores, we algorithmically analyze these predictions for cases where protein backbone exhibits rare topological complexity, that is, knotting. Amongst others, discovered a 7
Abstract In an effort to understand skyrmion behavior on a coarse-grained level, skyrmions are often described as 2D quasiparticles evolving according the Thiele equation. Interaction potentials key missing parameters for predictive modeling of experiments. Here, Iterative Boltzmann Inversion technique commonly used in soft matter simulations is applied construct skyrmion-skyrmion and skyrmion-magnetic material boundary interactions from single experimental measurement without any prior...
KNOTS (http://knots.mit.edu) is a web server that detects knots in protein structures. Several structures have been reported to contain intricate knots. The physiological role of and their effect on folding evolution an area active research. user submits PDB id or uploads 3D structure mmCIF format. current implementation the uses Alexander polynomial detect results analysis are presented location knot structure, type interactive visualization knot. can also be downloaded viewed offline....