Search results for "Biomolecule"
showing 10 items of 666 documents
The escape transition of a compressed star polymer: Self-consistent field predictions tested by simulation
2013
The escape transition of a polymer "mushroom" (a flexible chain grafted to a flat non-adsorbing substrate surface in a good solvent) occurs when the polymer is compressed by a cylindrical piston of radius $R$, that by far exceeds the chain gyration radius. At this transition, the chain conformation abruptly changes from a two-dimensional self-avoiding walk of blobs (of diameter $H$, the height of the piston above the substrate) to a "flower conformation", i.e. stretched almost one-dimensional string of blobs (with end-to-end distance $\approx R$) and an "escaped" part of the chain, the "crown", outside the piston. The extension of this problem to the case of star polymers with $f$ arms is c…
Non coaxial force and inductance calculations for bitter coils and coils with uniform radial current distributions
2011
Recently the Bessel function approach to calculating the magnetic fields of coils has been used to calculate the mutual inductance and the force between two non coaxial thick cylindrical coils with parallel axes and uniform radial current distributions. This method can also be applied to calculate the force and inductance between an ordinary coil and a Bitter coil, or between two bitter coils, not necessarily coaxial. Bitter coils give a simpler case of the method, and it is possible to solve analytically for the magnetic field of a bitter disk.
Physical Origin of Anharmonic Dynamics in Proteins: New Insights From Resolution-Dependent Neutron Scattering on Homomeric Polypeptides
2012
Neutron scattering reveals a complex dynamics in polypeptide chains, with two main onsets of anharmonicity whose physical origin and biological role are still debated. In this study the dynamics of strategically selected homomeric polypeptides is investigated with elastic neutron scattering using different energy resolutions and compared with that of a real protein. Our data spotlight the dependence of anharmonic transition temperatures and fluctuation amplitudes on energy resolution, which we quantitatively explain in terms of a two-site model for the protein-hydration water energy landscape. Experimental data strongly suggest that the protein dynamical transition is not a mere resolution …
Raman and Infrared Spectra of Acoustical, Functional Modes of Proteins from All-Atom and Coarse-Grained Normal Mode Analysis
2018
The directions of the largest thermal fluctuations of the structure of a protein in its native state are the directions of its low-frequency modes (below 1 THz), named acoustical modes by analogy with the acoustical phonons of a material. The acoustical modes of a protein assist its conformational changes and are related to its biological functions. Low-frequency modes are difficult to detect experimentally. A survey of experimental data of low-frequency modes of proteins is presented. Theoretical approaches, based on normal mode analysis, are of first interest to understand the role of the acoustical modes in proteins. In this chapter, the fundamentals of normal mode analysis using all-ato…
A proposed quantum mechanics mechanism for (e−, h+) charges separation applied to photosynthesis and energy production efficiency improovement
2009
Based on concepts in semiconductor band gap engineering (the staggered one), a qualitative model is proposed for the first step mechanism in artificial catalysis and natural systems such as photosynthesis in green leaves.
Comparison of Dissipative Particle Dynamics and Langevin thermostats for out-of-equilibrium simulations of polymeric systems
2007
In this work we compare and characterize the behavior of Langevin and Dissipative Particle Dynamics (DPD) thermostats in a broad range of non-equilibrium simulations of polymeric systems. Polymer brushes in relative sliding motion, polymeric liquids in Poiseuille and Couette flows, and brush-melt interfaces are used as model systems to analyze the efficiency and limitations of different Langevin and DPD thermostat implementations. Widely used coarse-grained bead-spring models under good and poor solvent conditions are employed to assess the effects of the thermostats. We considered equilibrium, transient, and steady state examples for testing the ability of the thermostats to maintain const…
NOISE EFFECTS IN POLYMER DYNAMICS
2008
The study of the noise induced effects on the dynamics of a chain molecule crossing a potential barrier, in the presence of a metastable state, is presented. A two-dimensional stochastic version of the Rouse model for a flexible polymer has been adopted to mimic the molecular dynamics and to take into account the interactions between adjacent monomers. We obtain a nonmonotonic behavior of the mean first passage time and its standard deviation, of the polymer centre of inertia, with the noise intensity. These findings reveal a noise induced effect on the mean crossing time. The role of the polymer length is also investigated.
Bridging the Gap Between Atomistic and Coarse-Grained Models of Polymers: Status and Perspectives
2000
Recent developments that increase the time and distance scales accessible in the simulations of specific polymers are reviewed. Several different techniques are similar in that they replace a model expressed in fully atomistic detail with a coarse-grained model of the same polymer, atomistic → coarse-grained (and beyond!), thereby increasing the time and distance scales accessible within the expenditure of reasonable computational resources. The bridge represented by the right-pointing arrow can be constructed via different procedures, which are reviewed here. The review also considers the status of methods which reverse this arrow, atomistic ← coarse-grained. This “reverse-mapping” recover…
New Development of Monte Carlo Techniques for Studying Bottle-brush Polymers
2011
Due to the complex characteristics of bottle-brush polymers, it became a challenge to develop an efficient algorithm for studying such macromolecules under various solvent conditions or some constraints in the space by using computer simulations. In the limit of a bottle-brush polymer with a rather stiff backbone (straight rigid backbone), we generalize the variant of the biased chain growth algorithm, the pruned-enriched Rosenbluth method, for simulating polymers with complex architecture, from star polymers to bottle-brush polymers, on the simple cubic lattice. With the high statistics of our Monte Carlo results, we check the theoretical predictions of side chain behavior and radial monom…
Force-dependent folding pathways in mechanically interlocked calixarene dimers via atomistic force quench simulations
2020
Single-molecule force spectroscopy and molecular simulations are well-established techniques to study the mechanical unfolding of supramolecular complexes in various fields of biomolecular physics....