Related papers: The dynamical transition in proteins and non-Gauss…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
We study the model of a molecular switch comprised of a molecule with a soft vibrational degree of freedom coupled to metallic leads. In the presence of strong electron-ion interaction, different charge states of the molecule correspond to…
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To…
We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures…
The layered semiconductor SnSe is one of the highest-performing thermoelectric materials known. We demonstrate, through a first-principles lattice-dynamics study, that the high-temperature Cmcm phase is a dynamic average over lower-symmetry…
The description of states and dynamics in non-Hermitian systems is fundamentally linked to the choice of an appropriate theoretical framework -- a point of ongoing debate in the field. This work addresses this issue by proposing a…
The Fenna Mathews Olson (FMO) complex of green sulphur bacteria is an example of a photosynthetic pigment protein complex, in which the electronic properties of the pigments are modified by the protein environment to promote efficient…
Inhomogeneous polymers play an important role in various cellular processes, both in nature and in biotechnological applications. At finite temperatures, inhomogeneous polymers exhibit non-trivial thermal fluctuations. In a broader context,…
Mossbauer spectroscopy and neutron scattering measurements on proteins embedded in solvents including water and aqueous mixtures have emphasized the observation of the distinctive temperature dependence of the atomic mean square…
Previous studies have suggested a crossover from superdiffusive to normal heat transport in one-dimensional (1D) anharmonic oscillator systems with a double-well type interatomic interaction like $V(\xi)=-\xi^2/2+\xi^4/4$, when the system…
Thermal shift assays (TSAs) have been extensively used to study thermodynamics of proteins and provide an efficient means to assess protein-ligand binding or protein-protein interaction. However, existing TSAs have limitations such as time…
We used various analytical and numerical techniques to elucidate signal propagation in a small enzymatic cascade which is subjected to external and internal noise. The nonlinear character of catalytic reactions, which underlie protein…
A theoretical study of the variation of thermodynamic and transport properties of calamitic liquid crystals across the isotropic-nematic phase transition is carried out by calculating the {\it wavenumber (k) and time (t)} dependent…
The rates of protein folding with photon absorption or emission and the cross section of photon -protein inelastic scattering are calculated from the quantum folding theory by use of standard field-theoretical method. All these protein…
The circadian clock can adapt itself to external cues, but the molecular mechanisms and regulatory networks governing circadian oscillations' transient adjustments are still largely unknown. Here we consider the specific case of circadian…
The dynamics of spin-boson systems at very low temperatures has been studied using a real-time path-integral simulation technique which combines a stochastic Monte Carlo sampling over the quantum fluctuations with an exact treatment of the…
Commonly, thermal transport properties of one-dimensional systems are found to be anomalous. Here, we perform a numerical and theoretical study of the $\beta$-FPUT chain, considered a prototypical model for one-dimensional anharmonic…
Vibrational energy relaxation (VER) of a selected mode in cytochrome c (hemeprotein) in vacuum is studied using two theoretical approaches: One is the equilibrium simulation approach with quantum correction factors, and the other is the…
The temperature dependence of thermodynamic and mechanical properties of six fcc transition metals (Ni, Cu, Ag, Au, Pt, Rh) and the alloying behavior of Ag-Au and Cu-Ni are studied using molecular dynamics (MD). The structures are described…
We study the spontaneous ''sliding'' of histone spools (nucleosomes) along DNA as a result of thermally activated single base pair twist defects. To this end we map the system onto a suitably extended Frenkel-Kontorova model. Combining…