Related papers: Fine structures of Intrinsically Disordered Protei…
We introduce a framework for model reduction of chain models for dissipative particle dynamics (DPD) simulations, where the characteristic size of the chain, pressure, density, and temperature are preserved. The proposed methodology reduces…
In a recent work we proposed a coarse-grained methodology for studying the response of peptides when simulated at different values of pH; in this work we extend the methodology to analyze the pH-dependent behavior of coiled coils. This…
Understanding the molecular mechanisms driving the binding between bio-molecules is a crucial challenge in molecular biology. In this respect, characteristics like the preferentially hydrophobic composition of the binding interfaces, the…
All-atom molecular dynamics (MD) computer simulations are a valuable tool for characterizing the conformational ensembles of intrinsically disordered proteins (IDPs). IDP conformational ensembles are highly heterogeneous and contain…
The interactions of a hydrophilic surface with water can significantly influence the characteristics of the liquid water interface. In this manuscript, we explore this influence by studying the molecular structure of liquid water at a…
Suspensions of Active Brownian Particles (ABP) undergo motility induced phase separation (MIPS) over a wide range of mean density and activity strength [1], even in the absence of an explicit attraction. Negative values of the mechanical…
Hypothesis A prototypical modelling approach is required for a full characterisation of the static and equilibrium dynamical properties of confined ionic liquids (ILs), in order to gain predictive power of properties that are difficult to…
Proteins are the major building blocks of life, and actuators of almost all chemical and biophysical events in living organisms. Their native structures in turn enable their biological functions which have a fundamental role in drug design.…
Considering a broad class of steady-state nonequilibrium systems for which some additive quantities are conserved by the dynamics, we introduce from a statistical approach intensive thermodynamic parameters (ITPs) conjugated to the…
We extend the incremental potential contact (IPC) model for contacting elastodynamics to resolve systems composed of codimensional DOFs in arbitrary combination. This enables a unified, interpenetration-free, robust, and stable simulation…
Motility-induced phase separation (MIPS) is a purely non-equilibrium phenomenon in which self-propelled particles phase separate without any attractive interactions. One surprising feature of MIPS is the emergence of polar, nematic, and…
The fragmentation of the Isoscalar Giant Quadrupole Resonance (ISGQR) in 40Ca has been investigated in high energy-resolution experiments using proton inelastic scattering at E_p = 200 MeV. Fine structure is observed in the region of the…
By exact computer enumeration and combinatorial methods, we have calculated the designability of proteins in a simple lattice H-P model for the protein folding problem. We show that if the strength of the non-additive part of the…
We combine small angle scattering experiments and simulations to investigate the internal structure and interactions of composite Poly(N-isopropylacrylamide)-Poly(ethylene glycol) (PNIPAM-PEG) microgels. At low temperatures the…
The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein-protein interactions is complicated by the fact that the…
Protein structure prediction has advanced significantly with the introduction of AlphaFold3, a diffusion-based model capable of predicting complex biomolecular interactions across proteins, nucleic acids, small molecules, and ions. While…
Random polyampholytes (PAs) contain positively and negatively charged monomers that are distributed randomly along the polymer chain. The interaction between charges is assumed to be given by the Debye-Huckel potential. We show that the…
Interacting-Particle Reaction Dynamics (iPRD) simulates the spatiotemporal evolution of particles that experience interaction forces and can react with one another. The combination of interaction forces and reactions enable a wide range of…
We discuss the reliability of integral-equation methods based on several commonly used closure relations in determining the phase diagram of coarse-grained models of soft-matter systems characterized by mutually interacting soft and…
Predicting favorable protein-peptide binding events remains a central challenge in biophysics, with continued uncertainty surrounding how nonlocal effects shape the global energy landscape. Here, we introduce peripheral surface information…