Related papers: Kinetic energy flows in activated dynamics of biom…
The response of proteins to chemical reactions or impulsive excitation that occurs within the molecule has fascinated chemists for decades. In recent years ultrafast X-ray studies have provided ever more detailed information about the…
In a variety of biological processes, eukaryotic cells use cilia to transport flow. Although cilia have a remarkably conserved internal molecular structure, experimental observations report very diverse kinematics. To address this…
The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…
We consider the energy current correlation function for the FPU-beta lattice. For small non-linearity one can rely on kinetic theory. The issue reduces then to a spectral analysis of the linearized collision operator. We prove thereby that,…
A theoretical framework is proposed for an energy decomposition scheme along the reaction coordinate, in which the ensemble average of the potential energy weighted with reactive flux intensity is decomposed into energy components at the…
Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…
Molecular motors fulfill critical functions within all living beings. Understanding their underlying working principles is therefore of great interest. Here we develop a simple model inspired by the two-component biomolecular motor Fo-F1…
Single molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different…
With the help of force spectroscopy, several analytical theories aim at estimating the rate coefficient of folding for various proteins. Nevertheless, a chief bottleneck lies in the fact that there is still no perfect consensus on how does…
Molecular machines transduce free energy between different forms throughout all living organisms. While truly machines in their own right, unlike their macroscopic counterparts molecular machines are characterized by stochastic…
It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…
Cells control fluid flows with a spatial and temporal precision that far exceeds the capabilities of current microfluidic technologies. Cells achieve this superior spatio-temporal control by harnessing dynamic networks of cytoskeleton and…
We investigate how nonlinearity and topological disorder affect the energy relaxation of local kicks in coarse-grained network models of proteins. We find that nonlinearity promotes long-range, coherent transfer of substantial energy to…
Incorporating the inherent heterogeneity of living systems into models of active nematics is essential to provide a more realistic description of biological processes such as bacterial growth, cell dynamics and tissue development.…
Kinetic approaches provide an effective description of the process of particle acceleration at shock fronts and allow to take into account the dynamical reaction of the accelerated particles as well as the amplification of the turbulent…
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…
We consider a second order gradient flow of the p-elastic energy for a planar theta-network of three curves with fixed lengths. We construct a weak solution of the flow by means of an implicit variational scheme. We show long-time existence…
In this paper we present a procedure to integrate, up to quadratures, the matching conditions of the energy shaping method. We do that in the context of underactuated Hamiltonian systems defined by simple Hamiltonian functions. For such…
Determining the different conformational states of a protein and the transition paths between them is key to fully understanding the relationship between biomolecular structure and function. This can be accomplished by sampling protein…
Biological molecular machines are bifunctional enzymes that catalyze two processes: one donating free energy and the other accepting it. Recent studies show that most protein enzymes have rich stochastic dynamics of transitions between the…