Search results for "Quantitative Biology::Biomolecules"
showing 10 items of 467 documents
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....
Isotope Effects and Collective Excitations
1983
Isotopic substitution in the aqueous solvent is discussed as an effective method for probing the role of solvent dynamics in the stability of biomolecular conformation.
Photophysical behavior of norharmane related to proximity effect
1990
Abstract Solvent and temperature effects of fluorescence and its polarization characteristics for norharmane were studied. From the results obtained it is concluded that the fluorescent state changes from the φφ ∗ -type in a polar solvent (EPA) to nφ ∗ -type in a nonpolar solvent (MC), and also that lowest singlet excited states (φφ ∗ -type and nφ ∗ -type) interact by vibronic coupling. In the nonpolar solvent (MC) the lowest singlet excited states are very close in energy and consequently the vibronic coupling is stronger. At high temperatures, in a nonpolar solvent (MC), the emission is from both the φφ ∗ - and nφ ∗ -states due to thermal equilibration, while at low temperatures the emiss…
Mapping CO diffusion paths in Myoglobin with the Single Sweep Method
2010
The pathways of diffusion and escape of a CO molecule inside and out a myoglobin protein are investigated. Specifically, the three-dimensional potential of mean force (PMF or free energy) of the CO molecule position inside the protein is calculated by using the single-sweep method in concert with fully resolved atomistic simulations in explicit solvent.The results are interpreted under the assumption that the diffusion of the ligand can be modeled as a navigation on the PMF in which the ligand hops between the PMF local minima following the minimum free energy paths (MFEPs) with rates set by the free energy barriers that need to be crossed. We calculate all these quantities --local minima, …