Related papers: Exactly Solvable Model for Helix-Coil-Sheet Transi…
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…
Hamiltonian dynamical systems possessing equilibria of ${saddle} \times {centre} \times...\times {centre}$ stability type display \emph{reaction-type dynamics} for energies close to the energy of such equilibria; entrance and exit from…
In this paper we present a derivation and multiscale analysis of a mathematical model for plant cell wall biomechanics that takes into account both the microscopic structure of a cell wall coming from the cellulose microfibrils and the…
We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…
The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover,…
Applying the contact density chain-growth algorithm to lattice heteropolymers, we identify the conformational transitions of a nongrafted hydrophobic-polar heteropolymer with 103 residues in the vicinity of a polar, a hydrophobic, and a…
We study transition paths in energy landscapes over multi-categorical Potts configurations using the mean-field approach introduced by Mauri et al., {\em Phys Rev Lett 130, 158402 (2023)}. Paths interpolate between two fixed configurations…
To understand the mechanism allowing for long-term storage of excess energy in proteins, we study a Hamiltonian system consisting of several coupled pendula in partial contact with a heat bath. It is found that energy absorption and storage…
We investigate the mechanisms underlying selective molecular recognition of single heteropolymers at chemically structured planar surfaces. To this end, we study systems with two-letter (HP) lattice heteropolymers by exact enumeration…
A four states phase diagram for protein folding as a function of temperature and solvent quality is derived from an improved 2-d lattice model taking into account the temperature dependence of the hydrophobic effect. The phase diagram…
We provide a complete thermodynamic solution of a 1D hopping model in the presence of a random potential by obtaining the density of states. Since the partition function is related to the density of states by a Laplace transform, the…
We introduce a soliton model to describe conformational structure of poly(oxyethylene) in aqueous solution. The model is based on former investigations for twistons in polyethylene, and the soliton solution corresponds to stable excitation…
A cubic structure of polymer colloid complexes is studied. The technique of the research includes i) an analysis of well-known literature SAXS data; on this base, at some assumptions, ii) constructing a simple model to estimate geometric…
Nearly a quarter of genomic sequences and almost half of all receptors that are likely to be targets for drug design are integral membrane proteins. Understanding the detailed mechanisms of the folding of membrane proteins is a largely…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
The Cahn-Hilliard equation and extensions, notably the Cahn-Hilliard-Darcy and Cahn-Hilliard-Navier-Stokes systems, provide widely used frameworks for coupling interfacial thermodynamics with flow. This review surveys the thermodynamic…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
Helices are the quintessential geometric motif of the microscale, from alpha-helices in proteins to double helices in DNA. Assembly of the helical geometry of biopolymers is a foundational step in a hierarchy of structure that eventually…
Simplicial complex (SC) representation is an elegant mathematical framework for representing the effect of complexes or groups with higher-order interactions in a variety of complex systems ranging from brain networks to social…
Breathing transitions represent recently discovered adsorption-induced structural transformations between large-pore and narrow-pore conformations in bistable metal-organic frameworks, such as MIL-53. We present a multiscale physical…