Related papers: Exactly Solvable Model for Helix-Coil-Sheet Transi…
Epigenetic histone modifications play an important role in the maintenance of different cell phenotypes. The exact molecular mechanism for inheritance of the modification patterns over cell generations remains elusive. We construct a…
We present a lattice model for polymer solutions, explicitly incorporating interactions with a bath of solvent and cosolvent molecules. By exploiting the well-known analogy between polymer systems and the $O(n)$-vector spin model in the…
We propose a model for motor proteins based on a hierarchical Hamiltonian that we have previously introduced to describe protein folding. The proposed motor model has high efficiency and is consistent with a linear load-velocity response.…
Based on the Zimm-Bragg model we study cooperative helix-coil transition driven by a finite-speed change of temperature. There is an asymmetry between the coil-to-helix and helix-to-coil transition: the latter is displayed already for…
Biological molecules can form hydrogen bonds between nearby residues, leading to helical secondary structures. The associated reduction of configurational entropy leads to a temperature dependence of this effect: the "helix-coil…
In this work, the nonequilibrium pathways of the collapse of the helix-forming biopolymer polyalanine are investigated. To this end, the full time evolution of the helix-coil transition is simulated using molecular dynamics simulations. At…
We construct the exact partition function of the Potts model on a complete graph subject to external fields with linear and nematic type couplings. The partition function is obtained as a solution to a linear diffusion equation and the free…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site correlations that arise from physical interactions between neighboring amino acid…
Proteins are fundamental biological entities mediating key roles in cellular function and disease. This paper introduces a multi-scale graph construction of a protein -- HoloProt -- connecting surface to structure and sequence. The surface…
Hydrogen's growing role in the transition towards climate-neutral energy systems necessitates structured modeling frameworks. Existing gas network models, largely developed for natural gas, fail to capture hydrogen systems distinct…
The conformations of semiflexible (bio)polymers are studied in flow through geometrically structured microchannels. Using mesoscale hydrodynamics simulations, we show that the polymer undergoes a rod-to-helix transition as it moves from the…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
An important open problem in materials science is whether a direct connection exists between single-particle elastic properties and the macroscopic bulk behavior. Here we address this question by focusing on the archetype of soft colloids:…
With this contribution, we give a complete and comprehensive framework for modeling the dynamics of complex mechanical structures as port-Hamiltonian systems. This is motivated by research on the potential of lightweight construction using…
We report a systematic investigation on the high-temperature thermoelectric response in a typical filling-control Mott transition system La1-xSrxVO3. In the vicinity of the Mott transition, incoherent charge transport appears with…
The practical use of non-Hermitian (i.e., typically, PT-symmetric) phenomenological quantum Hamiltonians is discussed as requiring an explicit reconstruction of the {\em ad hoc} Hilbert-space metrics which would render the time-evolution…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
We propose a rigorous approach of Semi-Infinite lattice systems illustrated with the study of surface transitions of the semi-infinite Potts model.
We implement the replica exchange molecular dynamics algorithm to study the interactions of a model peptide (WALP-16) with an explicitly represented DPPC membrane bilayer. We observe the spontaneous, unbiased insertion of WALP-16 into the…