相关论文: Universality of fold-encoded localized vibrations …
In vitro velocities of several cell types have been measured using computer controlled video microscopy, which allowed to record the cells' trajectories over several days. On the basis of our large data sets we show that the locomotion…
We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…
Modeling and simulating the protein folding process overall remains a grand challenge in computational biology. We systematically investigate end-to-end quantum algorithms for simulating various protein dynamics with effects, such as…
To design molecular spin qubits with enhanced quantum coherence, a control of the coupling between the local vibrations and the spin states is crucial, which could be realized in principle by engineering molecular structures via…
A mechanism for relationship of solvent viscosity with reaction rate constant at enzyme action is suggested. It is based on fluctuations of electric field in enzyme active site produced by thermally equilibrium rocking (cranckshaft motion)…
Understanding how the effectiveness of natural photosynthetic energy harvesting systems arises from the interplay between quantum coherence and environmental noise represents a significant challenge for quantum theory. Recently it has begun…
Arbitrary waves incident on a solid embedded nanoparticle are studied. The acoustic vibrational frequencies are shown to correspond to the poles of the scattering cross section in the complex frequency plane. The location of the poles is…
Proteins in organisms, rather than act alone, usually form protein complexes to perform cellular functions. We analyze the topological network structure of protein complexes and their component proteins in the budding yeast in terms of the…
The rate-limiting step of some enzymatic reactions is a physical step, i.e. diffusion. The efficiency of such reactions can be improved through an increase in the arrival rate of the substrate molecules, e.g. by a directed passage of…
Natural protein molecules are exceptional polymers. Encoded in apparently random strings of amino-acids, these objects perform clear physical tasks that are rare to find by simple chance. Accurate folding, specific binding, powerful…
Enzymes are on the front lines of evolution. All living organisms rely on highly efficient, specific enzymes for growth, sustenance, and reproduction; and many diseases are a consequence of a mutation on an enzyme that affects its catalytic…
Cells generally convert nutrient resources to useful products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although…
The natural vibrational frequencies of biological particles such as viruses and bacteria encode critical information about their mechanical and biological states as they interact with their local environment and undergo structural…
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence…
Catalysis lies at the heart of chemical reactivity, yet its foundational principles remain fragmented across the distinct domains of homogeneous, heterogeneous, and enzymatic systems Here, we propose a unifying theoretical model that…
Enzyme-enriched condensates can organize the spatial distribution of their substrates by catalyzing non-equilibrium reactions. Conversely, an inhomogeneous substrate distribution induces enzyme fluxes through substrate-enzyme interactions.…
Enzymes have been shown to diffuse faster in the presence of their reactants. Recently, we revealed new insights into this process of enhanced diffusion using single-particle tracking (SPT) with total internal reflection fluorescence (TIRF)…
We show, through analytical theory and rigorous numerical calculations, that optical binding can organize a collection of particles into stable one-dimensional lattice. This lattice, as well as other optically-bound structures, are shown to…
Natural proteins fold to a unique, thermodynamically dominant state. Modeling of the folding process and prediction of the native fold of proteins are two major unsolved problems in biophysics. Here, we show successful all-atom ab initio…
A local equilibrium approach for the kinetics of a simplified protein folding model, whose equilibrium thermodynamics is exactly solvable, was developed in [M. Zamparo and A. Pelizzola, Phys. Rev. Lett. 97, 068106 (2006)]. Important…