相关论文: Cooperative long range protein-protein dynamics in…
We extend the Saffman theory of membrane hydrodynamics to account for the correlated motion of membrane proteins, along with the effect of protein concentration on that correlation and on the response of the membrane to stresses.…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
We consider the lateral diffusion of a protein interacting with the curvature of the membrane. The interaction energy is minimized if the particle is at a membrane position with a certain curvature that agrees with the spontaneous curvature…
Mechanical unfolding of polyproteins by force spectroscopy provides valuable insight into their free energy landscapes. Most phenomenological models of the unfolding process are two-state and/or one dimensional, with the details of the…
Interactions mediated by the cell membrane between inclusions, such as membrane proteins or antimicrobial peptides, play important roles in their biological activity. They also constitute a fascinating challenge for physicists, since they…
The phonon-assisted sticking rate of slow moving atoms impinging on an elastic membrane at nonzero temperature is studied analytically using a model with linear atom-phonon interactions, valid in the weak coupling regime. A perturbative…
This paper focuses on mechanical aspects of chromatin biological functioning. Within a basic geometric modeling of the chromatin assembly, we give for the first time the complete set of elastic constants (twist and bend persistence lengths,…
Spectrally-peaked proton beams ($E_{p}\approx 8$ MeV, $\Delta E\approx 4$ MeV) have been observed from the interaction of an intense laser ($> 10^{19 }$ Wcm$^{-2}$) with ultrathin CH foils, as measured by spectrally-resolved full beam…
Molecules constitute compact hybrid quantum optical systems that can interface photons, electronic degrees of freedom, localized mechanical vibrations and phonons. In particular, the strong vibronic interaction between electrons and nuclear…
While solid-state protein junctions have shown efficient electron transport over lengths that surpass those of conventional organic semiconducting systems, interfacial or contact effects may obscure the intrinsic protein charge transport…
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…
We propose a theoretical framework for the detection of order parameter fluctuations in three dimensions using ultrafast coherent phonon spectroscopy. We focus our attention on long wavelength charge density fluctuations (plasmons), and…
The role of the rigidity of a peptide chain in its equilibrium dynamics is investigated within a realistic model with stringent microscopically derived coupling interaction potential and effective on-site potential. The coupling interaction…
Atomic undercoordination, charge injection, mechanical and thermal activation mediate the properties of a material intrinsically by bond relaxation from one equilibrium to another while the phonon spectrometrics probes the ever-unexpected…
Black phosphorus (BP) exhibits highly anisotropic properties and dynamical behavior that are unique even among two-dimensional and van der Waals (vdW) layered materials. Here, we show that an interlayer lattice contraction and concerted,…
We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…
We study two identical fermions, or two hard-core bosons, in an infinite chain and coupled to phonons by interactions that modulate their hopping as described by the Peierls/Su-Schrieffer-Heeger (SSH) model. We show that exchange of phonons…
Within a case study on the protein-protein interaction network (PIN) of Drosophila melanogaster we investigate the relation between the network's spectral properties and its structural features such as the prevalence of specific subgraphs…
We study the formation of protein-protein encounter complexes with a Langevin equation approach that considers direct, steric and thermal forces. As three model systems with distinctly different properties we consider the pairs…
The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure, or of wider and sometimes highly elaborated motions. Coarse-grained elastic-network descriptions are…