Calculation of the entropy and free energy of peptides by molecular dynamics simulations using the hypothetical scanning molecular dynamics method

Hypothetical scanning (HS) is a method for calculating the absolute entropy S and free energy F from a sample generated by any simulation technique. With this approach each sample configuration is reconstructed with the help of transition probabilities (TPs) and their product leads to the configuration's probability, hence to the entropy. Recently a new way for calculating the TPs by Monte Carlo (MC) simulations has been suggested, where all system interactions are taken into account. Therefore, this method--called HSMC--is in principle exact where the only approximation is due to insufficient sampling. HSMC has been applied very successfully to liquid argon, TIP3P water, self-avoiding walks on a lattice, and peptides. Because molecular dynamics (MD) is considered to be significantly more efficient than MC for a compact polymer chain, in this paper HSMC is extended to MD simulations as applied to peptides. Like before, we study decaglycine in vacuum but for the first time also a peptide with side chains, (Val)(2)(Gly)(6)(Val)(2). The transition from MC to MD requires implementing essential changes in the reconstruction process of HSMD. Results are calculated for three microstates, helix, extended, and hairpin. HSMD leads to very stable differences in entropy TDeltaS between these microstates with small errors of 0.1-0.2 kcal/mol (T=100 K) for a wide range of calculation parameters with extremely high efficiency. Various aspects of HSMD and plans for future work are discussed.     

Free volume hypothetical scanning molecular dynamics method for the absolute free energy of liquids

The hypothetical scanning (HS) method is a general approach for calculating the absolute entropy, S, and free energy, F, by analyzing Boltzmann samples obtained by Monte Carlo (MC) or molecular dynamics (MD) techniques. With HS applied to a fluid, each configuration i of the sample is reconstructed by gradually placing the molecules in their positions at i using transition probabilities (TPs). With our recent version of HS, called HSMC-EV, each TP is calculated from MC simulations, where the simulated particles are excluded from the volume reconstructed in previous steps. In this paper we remove the excluded volume (EV) restriction, replacing it by a "free volume" (FV) approach. For liquid argon, HSMC-FV leads to an improvement in efficiency over HSMC-EV by a factor of 2-3. Importantly, the FV treatment greatly simplifies the HS implementation for liquids, allowing a much more natural application of the method for MD simulations. Given the success and popularity of MD, the present development of the HSMD method for liquids is an important advancement for HS methodology. Results for the HSMD-FV approach presented here agree well with our HSMC and thermodynamic integration results. The efficiency of HSMD-FV is equivalent to HSMC-EV. The potential use of HSMC(MD)-FV in protein systems with explicit water is discussed.     

The stochastic models method applied to the critical behavior of Ising lattices

The stochastic models (SM) computer simulation method for treating manybody systems in thermodynamic equilibrium is investigated. The SM method, unlike the commonly used Metropolis Monte Carlo method, is not of a relaxation type. Thus an equilibrium configuration is constructed at once by adding particles to an initiallyempty volume with the help of a model stochastic process. The probability of the equilibrium configurations is known and this permits one to estimate the entropy directly. In the present work we greatly improve the accuracy of the SM method for the two and three-dimensional Ising lattices and extend its scope to calculate fluctuations, and hence specific heat and magnetic susceptibility, in addition to average thermodynamic quantities like energy, entropy, and magnetization. The method is found to be advantageous near the critical temperature. Of special interest are the results at the critical temperature itself, where the Metropolis method seems to be impractical. At this temperature, the average thermodynamic quantities agree well with theoretical values, for both the two and three-dimensional lattices. For the two-dimensional lattice the specific heat exhibits the expected logarithmic dependence on lattice size; the dependence of the susceptibility on lattice size is also satisfactory, leading to a ratio of critical exponents/=1.85 ±0.08. For the three-dimensional lattice the dependence of the specific heat, long-range order, and susceptibility on lattice size leads to similarly satisfactory exponents:=0.12 ±0.03,=0.30 ±0.03, and=1.32 ±0.05 (assuming =2/3).     

Internal field switching in CdSe quantum dot films on Si

If a thin film (tens of nm) of CdSe quantum dots (4 nm diameter) is deposited by chemical bath deposition onto various substrates, the films, although essentially intrinsic, behave as if they were n-type with respect to charge separation. However, films deposited under certain deposition conditions on Si (both n(+)- and p(+)-type) behave as if they were p-type. In this case, we show that it is possible to switch this p-type photoresponse by either light illumination intensity or injection of electrons from an external filament. Using both surface photovoltage spectroscopy and a novel adaptation of X-ray photoelectron spectroscopy, we show how this behavior results from a Cd(OH)(2) layer adsorbed at the Si surface at the beginning of the deposition. This response is explained by a competition between a high concentration of relatively shallow hole traps in the CdSe and a lower concentration of deeper electron traps in the Cd(OH)(2). The relative occupancies of these traps determine the fields in the film and their response to external parameters.     

Effect of molecular binding to a semiconductor on metal/molecule/semiconductor junction behavior

Diodes made by (indirectly) evaporating Au on a monolayer of molecules that are adsorbed chemically onto GaAs, via either disulfide or dicarboxylate groups, show roughly linear but opposite dependence of their effective barrier height on the dipole moment of the molecules. We explain this by Au-molecule (electrical) interactions not only with the exposed end groups of the molecule but also with its binding groups. We arrive at this conclusion by characterizing the interface by in situ UPS-XPS, ex situ XPS, TOF-SIMS, and Kelvin probe measurements, by scanning microscopy of the surfaces, and by current-voltage measurements of the devices. While there is a very limited interaction of Au with the dicarboxylic binding groups, there is a much stronger interaction with the disulfide groups. We suggest that these very different interactions lead to different (growth) morphologies of the evaporated gold layer, resulting in opposite effects of the molecular dipole on the junction barrier height.     

A Monte Carlo study of the entropy,the pressure,and the critical behavior of the hard-square lattice gas

An approximate technique for estimating the entropyS with computer simulation methods, suggested recently by Meirovitch, is applied here to the Metropolis Monte Carlo (MC) simulation of the hard-square lattice gas in both the grand canonical and the canonical ensembles. The chemical potentialμ, calculated by Widom's method, andS enable one to obtain also the pressureP. The MC results are compared with results obtained with Padé approximants (PA) and are found to be very accurate; for example, at the critical activityz _c the MC and the PA estimates forS deviate by 0.5%. Beyondz _c this deviation decreases to 0.01% and comparable accuracy is detected forP. We argue that close toz _c our results forS, μ, andP are more accurate than the PA estimates. Independent of the entropy study, we also calculate the critical exponents by applying Fisher's finite-size scaling theory to the results for the long-range order, the compressibility and the staggered compressibility, obtained for several lattices of different size at z_c. The data are consistent with the critical exponents of the plane Ising latticeβ=1/8,ν=1,γ=7/4, andα=0. Our values forβ and ν agree with series expansion and renormalization group results, respectively,α=0 has been obtained also by matrix method studies; it differs, however, from the estimate of Baxteret al. α=0.09 ± 0.05. As far as we knowγ has not been calculated yet.     

A marked synergistic effect in antitumor activity of salan titanium(IV) complexes bearing two differently substituted aromatic rings

Salan titanium(IV) complexes of differently substituted aromatic rings, where one ring is para-nitrated and another is ortho,para-halogenated, demonstrate exceptionally high anticancer activity, with IC(50) values of <1 μM, exceeding that of cisplatin by ~30-fold. Whereas an additive effect in hydrolytic stability was detected for these highly stable complexes, an unexpected synergistic effect in anticancer activity makes these hybrid complexes substantially more active than both their symmetrical analogues alone and their equimolar mixture.     

Approximation algorithms for group prize-collecting and location-routing problems

In this paper we develop approximation algorithms for generalizations of the following three known combinatorial optimization problems, the Prize-Collecting Steiner Tree problem, the Prize-Collecting Travelling Salesman Problem and a Location-Routing problem.Given a graph G=(V,E) on n vertices and a length function on its edges, in the grouped versions of the above mentioned problems we assume that V is partitioned into k+1 groups, {V₀,V₁,…,V_k}, with a penalty function on the groups. In the Group Prize-Collecting Steiner Tree problem the aim is to find S, a collection of groups of V and a tree spanning the rest of the groups not in S, so as to minimize the sum of the costs of the edges in the tree and the costs of the groups in S. The Group Prize-Collecting Travelling Salesman Problem, is defined analogously. In the Group Location-Routing problem the customer vertices are partitioned into groups and one has to select simultaneously a subset of depots to be opened and a collection of tours that covers the customer groups. The goal is to minimize the costs of the tours plus the fixed costs of the opened depots. We give a -approximation algorithm for each of the three problems, where I is the cardinality of the largest group.     

Angular broadening in core‐electron spectroscopy

The role of angular broadening in quantitative core‐electron spectroscopy is investigated using an analytic approach. It is shown why, practically, this effect remains relatively small for a broad range of parameters. A correction factor is derived, suggesting that the replacement of inelastic mean free path by an effective attenuation‐length parameter is not necessarily an optimal choice. The derived expression further proposes useful insight on the contribution of leading experimental parameters and, in particular, on the sharp increase of elastic‐scattering corrections above a (depth dependent) critical angle. Copyright © 2015 John Wiley & Sons, Ltd.