Related papers: Dissecting Ubiquitin Folding Using the Self-Organi…
Elucidation of possible pathways between folded (native) and unfolded states of a protein is a challenging task, as the intermediates are often hard to detect. Here we alter the solvent environment in a controlled manner by choosing two…
The motility of eukaryotic cells is strongly influenced by their environment, with confined cells often developing qualitatively different motility patterns from those migrating on simple two-dimensional substrates. Recent experiments,…
Molecular dynamics simulations of ultrathin water film confined between atomically flat rigid diamond plates are described. Films with thickness of one and two molecular diameters are concerned and TIP4P model is used for water molecules.…
We study a stationary Gibbs particle process with deterministically bounded particles on Euclidean space defined in terms of an activity parameter and non-negative interaction potentials of finite range. Using disagreement percolation we…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…
We propose a simple phenomenological model for describing the conformational dynamics of biopolymers via the nonlinearity-induced buckling and collapse (i.e. coiling up) instabilities. Taking into account the coupling between the internal…
The melting of ultrathin lubricant film is studied by friction between atomically flat surfaces. The fluctuations of lubricant temperature are taken into account defined by Ornstein-Uhlenbeck process. The phase diagrams and portraits are…
We propose that spontaneous folding and molecular evolution of biopolymers are two universal aspects that must concur for life to happen. These aspects are fundamentally related to the chemical composition of biopolymers and crucially…
Quantum states with long-lived coherence are essential for quantum computation, simulation and metrology. The nuclear spin states of ultracold molecules prepared in the singlet rovibrational ground state are an excellent candidate 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 calculate the effective Coulomb repulsion between electrons/holes, U, and site energy for an isolated BEDT-TTF [bis(ethylenedithio)tetrathiafulvalene] molecule in vacuo. U=4.2 \pm 0.1 eV for 44 experimental geometries taken from a broad…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Detailed thermodynamic analysis of complex systems with multiple stable configurational states allows for insight into the cooperativity of each individual transition. In this work we derive a heat capacity decomposition comprising…
Sliding phases have been long sought after in the context of coupled XY-models, as they are of relevance to various many-body systems such as layered superconductors, freestanding liquid-crystal films, and cationic lipid-DNA complexes. Here…
We discuss multiscale simulations of long biopolymer translocation through wide nanopores that can accommodate multiple polymer strands. The simulations provide clear evidence of folding quantization, namely, the translocation proceeds…
We present results of molecular dynamics (MD) simulations for a non-entangled polymer melt confined between two completely smooth and repulsive walls, interacting with inner particles via the potential $U_{\rm wall}\myeq (\sigma/z)^9$,…
The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial…
We introduce an ultrasoft core model of interpenetrating polycations and polyanions with continuous Gaussian charge distributions, to investigate polyelectrolyte aggregation in dilute and semi-dilute, salt-free solutions. The model is…
While the dynamics of polymer chains in equilibrium media is well understood by now, the polymer dynamics in active non-equilibrium environments can be very different. Here we study the dynamics of polymers in a viscous medium containing…
Among the unsolved problems in computational biology, protein folding is one of the most interesting challenges. To study this folding, tools like neural networks and genetic algorithms have received a lot of attention, mainly due to the…