Related papers: Behavior of H-FABP-fatty acid complex in a protein…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Polymer blends offer an exciting material for various potential applications due to their tunable properties by varying constituting components and their relative composition. Our simulation results unravel an intrinsic relationship between…
Crystallization of proteins, specifically proteins of medical relevance, is performed for various reasons such as to understand the protein structure and to design therapies. Obtaining kinetic constants in rate laws for nucleation and…
A low-temperature dynamical transition has been reported in several proteins. We provide the first observation of a `protein-like' dynamical transition in nonbiological aqueous environments. To this aim we exploit the popular colloidal…
Several short-chain fatty acids and their corresponding potential existing hydrated forms are important molecules in interstellar space. Their structures were optimized with twelve different computational methods. The dipole moments and the…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an…
PHAST is a software package written in standard Fortran, with MPI and CUDA extensions, able to efficiently perform parallel multicanonical Monte Carlo simulations of single or multiple heteropolymeric chains, as coarse-grained models for…
In this work, we study the dynamics of complex systems with time-dependent transition rates, focusing on $p$-adic analysis in modeling such systems. Starting from the master equation that governs the stochastic dynamics of a system with a…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those…
Protein crystal production is a major bottleneck for the structural characterisation of proteins. To advance beyond large-scale screening, rational strategies for protein crystallization are crucial. Understanding how chemical anisotropy…
Quantum kinetically constrained models can exhibit a wealth of dynamical phenomena ranging from anomalous transport to Hilbert-space fragmentation (HSF). We study a class of one-dimensional particle number conserving systems where particle…
From the crystal structure data and using the concept of equilbrium statistical mechanics we show how to calculate the thermodynamics of protein/DNA complexes. We apply the method to the TATA-box binding protein (TBP)/TATA sequence complex.…
Protein dynamics play a crucial role in many biological processes and drug interactions. However, measuring, and simulating protein dynamics is challenging and time-consuming. While machine learning holds promise in deciphering the…
From the point of view of statistical mechanics, a full characterisation of a molecular system requires the experimental determination of its possible states, their populations and the respective interconversion rates. Well-established…
Polymorphism has been observed in viral capsid assembly, demonstrating the ability of identical protein dimers to adopt multiple geometries under the same solution conditions. A well-studied example is the hepatitis B virus (HBV), which…
In order to increase the efficiency of the computer simulation of biological molecules, it is very common to impose holonomic constraints on the fastest degrees of freedom; normally bond lengths, but also possibly bond angles. However, as…