Effect of orientational motion of mobile chromophores on the dynamics of Forster energy transfer in polymers

Brownian dynamics (BD) simulations have been carried out to explore the effects of the orientational motion of the donor-acceptor (D-A) chromophore pair on the Forster energy transfer between the D-A pair embedded in a polymer chain in solution. It is found that the usually employed orientational averaging (that is, replacing the orientational factor, kappa, by kappa (2) = 2/3) may lead to an error in the estimation of the rate of the reaction by about 20%. In the limit of slow orientational relaxation, the preaveraging of the orientational factor leads to an overestimation of the rate, while in the opposite limit of very fast orientational relaxation, the usual scheme underestimates the rate. The latter results from an interesting interplay between reaction and diffusion. On the other hand, when one of the chromophores is fixed, the preaveraged rate is found to be fairly reliable if the rotational relaxation of the chromophore is sufficiently fast. The present study also reveals a power law dependence of the FRET rate on the chain length (rate proportional to N- alpha, with alpha approximate to 2.6).

On the dynamics of activation of mammalian X chromosomes

We have investigated a mathematical model of the process of activation of the X chromosomes in eutherian mammals. The model assumes that the activation is brought about over some definite time interval T by the complete saturation of N receptor sites on an X chromosome by M activating molecules (or multiples of M). The probability λ of a first hit on the receptor site is considered to be very much lower than that of subsequent hits; that is, we assume strong co-operative binding. Assuming further that an incomplete saturation of receptor sites is malfunctional, we can show that for proper activation of X chromosomes in normal diploid males and females, we must have λMT ≥ 3 and 0·96 ≤ N/M ≤ 1. An extension of this analysis for the triploid cases shows that under these conditions, we cannot explain the activation of two X's if the number of activating molecules is fixed at M. This suggests that there must be two classes of triploid embryos differing from each other in a step-wise manner in the number of activating molecules. In other words, triploids with two active X chromosomes would require 2M activating molecules as opposed to M molecules in triploids with a single active X. This interpretation of the two classes of triploids would be consistent with differing imprinting histories of the parental contributions to the triploid zygote.

Bidding Dynamics of Rational Advertisers in Sponsored Search Auctions on the Web

In this paper, we address a key problem faced by advertisers in sponsored search auctions on the web: how much to bid, given the bids of the other advertisers, so as to maximize individual payoffs? Assuming the generalized second price auction as the auction mechanism, we formulate this problem in the framework of an infinite horizon alternative-move game of advertiser bidding behavior. For a sponsored search auction involving two advertisers, we characterize all the pure strategy and mixed strategy Nash equilibria. We also prove that the bid prices will lead to a Nash equilibrium, if the advertisers follow a myopic best response bidding strategy. Following this, we investigate the bidding behavior of the advertisers if they use Q-learning. We discover empirically an interesting trend that the Q-values converge even if both the advertisers learn simultaneously.

Molecular Dynamics Perspective on the Protein Thermal Stability: A Case Study Using SAICAR Synthetase

The enzyme SAICAR synthetase ligates aspartate with CAIR (5'-phosphoribosyl-4-carboxy-5-aminoimidazole) forming SAICAR (5-amino-4-imidazole-N-succinocarboxamide ribonucleotide) in the presence of ATP. In continuation with our previous study on the thermostability of this enzyme in hyper-/thermophiles based on the structural aspects, here, we present the dynamic aspects that differentiate the mesophilic (E. coli, E. chaffeensis), thermophilic (G. kaustophilus), and hyperthermophilic (M. jannaschii, P. horikoshii) SAICAR synthetases by carrying out a total of 11 simulations. The five functional dimers from the above organisms were simulated using molecular dynamics for a period of 50 ns each at 300 K, 363 K, and an additional simulation at 333 K for the thermophilic protein. The basic features like root-mean-square deviations, root-mean-square fluctuations, surface accessibility, and radius of gyration revealed the instability of mesophiles at 363 K. Mean square displacements establish the reduced flexibility of hyper-/thermophiles at all temperatures. At the simulations time scale considered here, the long-distance networks are considerably affected in mesophilic structures at 363 K. In mesophiles, a comparatively higher number of short-lived (having less percent existence time) C alpha, hydrogen bonds, hydrophobic interactions are formed, and long-lived (with higher percentage existence time) contacts are lost. The number of time-averaged salt-bridges is at least 2-fold higher in hyperthermophiles at 363 K. The change in surface accessibility of salt-bridges at 363 K from 300 K is nearly doubled in mesophilic protein compared to proteins from other temperature classes.

Quantum chemical study on influence of intermolecular hydrogen bonding on the geometry, the atomic charges and the vibrational dynamics of 2,6-dichlorobenzonitrile

FT-IR (4000-400 cm(-1)) and FT-Raman (4000-200 cm(-1)) spectral measurements on solid 2,6-dichlorobenzonitrile (2,6-DCBN) have been done. The molecular geometry, harmonic vibrational frequencies and bonding features in the ground state have been calculated by density functional theory at the B3LYP/6-311++G (d,p) level. A comparison between the calculated and the experimental results covering the molecular structure has been made. The assignments of the fundamental vibrational modes have been done on the basis of the potential energy distribution (PED). To investigate the influence of intermolecular hydrogen bonding on the geometry, the charge distribution and the vibrational spectrum of 2,6-DCBN; calculations have been done for the monomer as well as the tetramer. The intermolecular interaction energies corrected for basis set superposition error (BSSE) have been calculated using counterpoise method. Based on these results, the correlations between the vibrational modes and the structure of the tetramer have been discussed. Molecular electrostatic potential (MEP) contour map has been plotted in order to predict how different geometries could interact. The Natural Bond Orbital (NBO) analysis has been done for the chemical interpretation of hyperconjugative interactions and electron density transfer between occupied (bonding or lone pair) orbitals to unoccupied (antibonding or Rydberg) orbitals. UV spectrum was measured in methanol solution. The energies and oscillator strengths were calculated by Time Dependent Density Functional Theory (TD-DFT) and matched to the experimental findings. TD-DFT method has also been used for theoretically studying the hydrogen bonding dynamics by monitoring the spectral shifts of some characteristic vibrational modes involved in the formation of hydrogen bonds in the ground and the first excited state. The C-13 nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge independent atomic orbital (GIAO) method and compared with experimental results. Standard thermodynamic functions have been obtained and changes in thermodynamic properties on going from monomer to tetramer have been presented. (C) 2013 Elsevier B.V. All rights reserved.

Mapping Post-translational Modifications of Mammalian Testicular Specific Histone Variant TH2B in Tetraploid and Haploid Germ Cells and Their Implications on the Dynamics of Nucleosome Structure

Histones regulate a variety of chromatin templated events by their post-translational modifications (PTMs). Although there are extensive reports on the PTMs of canonical histones, the information on the histone variants remains very scanty. Here, we report the identification of different PTMs, such as acetylation, methylation, and phosphorylation of a major mammalian histone variant TH2B. Our mass spectrometric analysis has led to the identification of both conserved and unique modifications across tetraploid spermatocytes and haploid spermatids. We have also computationally derived the 3-dimensional model of a TH2B containing nucleosome in order to study the spatial orientation of the PTMs identified and their effect on nucleosome stability and DNA binding potential. From our nucleosome model, it is evident that substititution of specific amino acid residues in TH2B results in both differential histone-DNA and histone-histone contacts. Furthermore, we have also observed that acetylation on the N-terminal tail of TH2B weakens the interactions with the DNA. These results provide direct evidence that, similar to somatic H2B, the testis specific histone TH2B also undergoes multiple PTMs, suggesting the possibility of chromatin regulation by such covalent modifications in mammalian male germ cells.

Influence of a Counterion on the Ion Atmosphere of an Anion: A Molecular Dynamics Study of LiX and CsX (X = F-, Cl-, I-) in Methanol

We report molecular dynamics (MD) simulations to explore the influence of a counterion on the structure and dynamics of cationic and anionic solvation shells for various ions in methanol at 298 K. We show that the variation in ionic size of either the cation or the anion in an ion pair influences the solvation structure of the other ion as well as the diffusivity in an electrolyte solution of methanol. The extent of ionic association between the cation and its counteranion of different ionic sizes has been investigated by analyzing the radial distribution functions (RDFs) and the orientation of methanol molecules in the first solvation shell (FSS) of ions. It is shown that the methanol in the FSS of the anion as well the cation exhibit quite different radial and orientational structures as compared to methanol which lie in the FSS of either the anion or the cation but not both. We find that the coordination number (CN) of F-, Cr-, and I- ions decreases with increasing size of the anion which is contrary to the trend reported for the anions in H2O. The mean residence time (MRT) of methanol molecules in the FSS of ions has been calculated using the stable states picture (SSP) approach. It is seen that the ion-counterion interaction has a considerable influence on the MRT of methanol molecules in the FSS of ions. We also discuss the stability order of the ion-counterion using the potentials of mean force (PMFs) for ion pairs with ions of different sizes. The PMF plots reveal that the Li+-F- pair (small-small) is highly stable and the Li+-I- pair is least stable (small-large) in electrolyte solutions.

On the critical thickness for non-localized to localized plastic flow transition in metallic glasses: A molecular dynamics study

Molecular dynamics simulations were employed to investigate the specimen thickness-dependent tensile behavior of a series of Cu(x)Z(100-x) (x = 20, 40, 50, 64 and 80 at%) metallic glass (MG) films, with a particular focus on the critical thickness, tc, below which non-localized plastic flow takes place. The simulation results reveal that while the transition occurs in all the alloys examined, t(c) is sensitive to the composition. We rationalize t(c) by postulating that the strain energy stored in the sample at the onset of plastic deformation has to be sufficient for the formation of shear bands. The composition-dependence of t(c) was found to correlate with the average activation energy of the atomic level plastic deformation events. (C) 2015 Elsevier Ltd. All rights reserved.

Insight into the Evaporation Dynamics of a Pair of Sessile Droplets on a Hydrophobic Substrate

In this work, we have demonstrated three unique regimes in the evaporation lifecycle of a pair of sessile droplets placed in variable proximity on a hydrophobic substrate. For small separation distance, the droplets undergo asymmetric spatiotemporal,evaporation leading to contact angle hysteresis and suppressed vaporization. The reduced evaporation has been attributed quantitatively to the existence of a constrained vapor-rich dome between the two droplets. However, a dynamic decrease in the droplet radius due to solvent removal marks a return to symmetry in terms of evaporation and contact angle. We have described the variation in evaporation flux using a universal correction factor. We have also demonstrated the existence of a critical separation distance beyond which the droplets in the, droplet pair do not affect each other. The results are crucial to a plethora of applications ranging from surface patterning to lab-on-a-chip devices.

Insight into the Evaporation Dynamics of a Pair of Sessile Droplets on a Hydrophobic Substrate

In this work, we have demonstrated three unique regimes in the evaporation lifecycle of a pair of sessile droplets placed in variable proximity on a hydrophobic substrate. For small separation distance, the droplets undergo asymmetric spatiotemporal,evaporation leading to contact angle hysteresis and suppressed vaporization. The reduced evaporation has been attributed quantitatively to the existence of a constrained vapor-rich dome between the two droplets. However, a dynamic decrease in the droplet radius due to solvent removal marks a return to symmetry in terms of evaporation and contact angle. We have described the variation in evaporation flux using a universal correction factor. We have also demonstrated the existence of a critical separation distance beyond which the droplets in the, droplet pair do not affect each other. The results are crucial to a plethora of applications ranging from surface patterning to lab-on-a-chip devices.

Molecular dynamics and simulations study on the vibrational and electronic solvatochromism of benzophenone

Solvent plays a key role in diverse physico-chemical and biological processes. Therefore, understanding solute-solvent interactions at the molecular level of detail is of utmost importance. A comprehensive solvatochromic analysis of benzophenone (Bzp) was carried out in various solvents using Raman and electronic spectroscopy, in conjunction with Density Functional Theory (DFT) calculations of supramolecular solute-solvent clusters generated using classical Molecular Dynamics Simulations (c-MDSs). The >C=O stretching frequency undergoes a bathochromic shift with solvent polarity. Interestingly, in protic solvents this peak appears as a doublet: c-MDS and ad hoc explicit solvent ab initio calculations suggest that the lower and higher frequency peaks are associated with the hydrogen bonded and dangling carbonyl group of Bzp, respectively. Additionally, the dangling carbonyl in methanol (MeOH) solvent is 4 cm(-1) blue-shifted relative to acetonitrile solvent, despite their similar dipolarity/polarizability. This suggests that the cybotactic region of the dangling carbonyl group in MeOH is very different from its bulk solvent structure. Therefore, we propose that this blue-shift of the dangling carbonyl originates in the hydrophobic solvation shell around it resulting from extended hydrogen bonding network of the protic solvents. Furthermore, the 1(1)n pi* (band I) and 1(1)pi pi* (band II) electronic transitions show a hypsochromic and bathochromic shift, respectively. In particular, these shifts in protic solvents are due to differences in their excited state-hydrogen bonding mechanisms. Additionally, a linear relationship is obtained for band I and the >C=O stretching frequency (cm(-1)), which suggests that the different excitation wavelengths in band I correspond to different solvation states. Therefore, we hypothesize that the variation in excitation wavelengths in band I could arise from different solvation states leading to varying solvation dynamics. This will have implications for ultrafast processes associated with electron-transfer, charge transfer, and also the photophysical aspects of excited states. (C) 2016 AIP Publishing LLC.

The role of lysine-41 in RNase A catalysis - A quantum chemical study on the active site ligand complex

Several mechanisms have been proposed to explain the action of enzymes at the atomic level. Among them, the recent proposals involving short hydrogen bonds as a step in catalysis by Gerlt and Gassman [1] and proton transfer through low barrier hydrogen bonds (LBHBs) [2, 3] have attracted attention. There are several limitations to experimentally testing such hypotheses, Recent developments in computational methods facilitate the study of active site-ligand complexes to high levels of accuracy, Our previous studies, which involved the docking of the dinucleotide substrate UpA to the active site of RNase A [4, 5], enabled us to obtain a realistic model of the ligand-bound active site of RNase A. From these studies, based on empirical potential functions, we were able to obtain the molecular dynamics averaged coordinates of RNase A, bound to the ligand UpA. A quantum mechanical study is required to investigate the catalytic process which involves the cleavage and formation of covalent bonds. In the present study, we have investigated the strengths of some of the hydrogen bonds between the active site residues of RNase A and UpA at the ab initio quantum chemical level using the molecular dynamics averaged coordinates as the starting point. The 49 atom system and other model systems were optimized at the 3-21G level and the energies of the optimized systems were obtained at the 6-31G* level. The results clearly indicate the strengthening of hydrogen bonds between neutral residues due to the presence of charged species at appropriate positions. Such a strengthening manifests itself in the form of short hydrogen bonds and a low barrier for proton transfer. In the present study, the proton transfer between the 2'-OH of ribose (from the substrate) and the imidazole group from the H12 of RNase A is influenced by K41, which plays a crucial role in strengthening the neutral hydrogen bond, reducing the barrier for proton transfer.

How does contrasting dependence of impurity-atom diffusivity on the density of host disordered medium arise?

We report results of molecular dynamics investigations into neutral impurity diffusing within an amorphous solid as a function of the size of the diffusant and density of the host amorphous matrix. We find that self diffusivity exhibits an anomalous maximum as a function of the size of the impurity species. An analysis of properties of the impurity atom with maximum diffusivity shows that it is associated with lower mean square force, reduced backscattering of velocity autocorrelation function, near-exponential decay of the intermediate scattering function (as compared to stretched-exponential decay for other sizes of the impurity species) and lower activation energy. These results demonstrate the existence of size-dependent diffusivity maximum in disordered solids. Further, we show that the diffusivity maximum is observed at lower impurity diameters with increase in density. This is explained in terms of the Levitation parameter and the void structure of the amorphous solid. We demonstrate that these results imply contrasting dependence of self diffusivity (D) on the density of the amorphous matrix, p. D increases with p for small sizes of the impurity but shows an increase followed by a decrease for intermediate sizes of the impurity atom. For large sizes of the impurity atom, D decreases with increase in p. These contrasting dependence arises naturally from the existence of Levitation Effect.

On the nature of power flow equations in security analysis

The power system network is assumed to be in steady-state even during low frequency transients. However, depending on generator dynamics, and toad and control characteristics, the system model and the nature of power flow equations can vary The nature of power flow equations describing the system during a contingency is investigated in detail. It is shown that under some mild assumptions on load-voltage characteristics, the power flow equations can be decoupled in an exact manner. When the generator dynamics are considered, the solutions for the load voltages are exact if load nodes are not directly connected to each other