Exploring High Dimensional Free Energy Landscapes: Temperature Accelerated Sliced Sampling

Biased sampling of collective variables is widely used to accelerate rare events in molecular simulations and to explore free energy surfaces. However, computational efficiency of these methods decreases with increasing number of collective variables, which severely limits the predictive power of the enhanced sampling approaches. Here we propose a method called Temperature Accelerated Sliced Sampling (TASS) that combines temperature accelerated molecular dynamics with umbrella sampling and metadynamics to sample the collective variable space in an efficient manner. The presented method can sample a large number of collective variables and is advantageous for controlled exploration of broad and unbound free energy basins. TASS is also shown to achieve quick free energy convergence and is practically usable with ab initio molecular dynamics techniques

Sampling Free Energy Surfaces as Slices by Combining Umbrella Sampling and Metadynamics

Metadynamics (MTD) is a very powerful technique to sample high-dimensional free energy landscapes, and due to its self-guiding property, the method has been successful in studying complex reactions and conformational changes. MTD sampling is based on filling the free energy basins by biasing potentials and thus for cases with flat, broad and unbound free energy wells, the computational time to sample them becomes very large. To alleviate this problem, we combine the standard Umbrella Sampling (US) technique with MTD to sample orthogonal collective variables (CVs) in a simultaneous way. Within this scheme, we construct the equilibrium distribution of CVs from biased distributions obtained from independent MTD simulations with umbrella potentials. Reweighting is carried out by a procedure that combines US reweighting and Tiwary-Parrinello MTD reweighting within the Weighted Histogram Analysis Method (WHAM). The approach is ideal for a controlled sampling of a CV in a MTD simulation, making it computationally efficient in sampling flat, broad and unbound free energy surfaces. This technique also allows for a distributed sampling of a high-dimensional free energy surface, further increasing the computational efficiency in sampling. We demonstrate the application of this technique in sampling high-dimensional surface for various chemical reactions using ab initio and QM/MM hybrid molecular dynamics simulations. Further, in order to carry out MTD bias reweighting for computing forward reaction barriers in ab initio or QM/MM simulations, we propose a computationally affordable approach that does not require recrossing trajectories

Mechanism and kinetics of Aztreonam hydrolysis catalyzed by class-C β-lactamase : a temperature-accelerated sliced sampling study

Enhanced sampling of large number of collective variables (CVs) is inevitable in molecular dynamics (MD) simulations of complex chemical processes such as enzymatic reactions. Because of the computational overhead of hybrid quantum mechanical/molecular mechanical (QM/MM)-based MD simulations, especially together with density functional theory, predictions of reaction mechanism, and estimation of free-energy barriers have to be carried out within few tens of picoseconds. We show here that the recently developed temperature-accelerated sliced sampling method allows one to sample large number of CVs, thereby enabling us to obtain rapid convergence in free-energy estimates in QM/MM MD simulation of enzymatic reactions. Moreover, the method is shown to be efficient in exploring flat and broad free-energy basins that commonly occur in enzymatic reactions. We demonstrate this by studying deacylation and reverse acylation reactions of aztreonam drug catalyzed by a class-C β lactamase (CBL) bacterial enzyme. Mechanistic details and nature of kinetics of aztreonam hydrolysis by CBL are elaborated here. The results of this study point to characteristics of the aztreonam drug that are responsible for its slow hydrolysis

Cash Flow Defining The Construction Industry

Cash flow is one of the most critical aspects in the proper management of any company or industry. Success or failure in proper cash flow management ultimately plays a huge role in determining the success or failure of the company or industry as a whole. Cash flow exists at three levels, the company management level, at an individual manager level and at the individual level in terms of productivity. Cash flow can be observed as a series of transactions in a game. The interesting feature in the game is that the state of no-move by one player, as in a failure to pay, may lead to a game-ending move for another player. Cash flow is not like productivity, it is not completely controlled by factors in the company’s control, and even the best-managed companies may experience liquidity problems from time to time. This research develops the game and the game rules to study cash flow at a microeconomic level. The game represents a real life scenario; the decisions are taken based on input data and prior knowledge. The game result is a cash flow model. The cash flow model provides input data for a statistical analysis of the output data. Most cash flow decisions are made by a manager with limited autonomy and often no real control occurs at the financial management level. The personal responsibility levels are moderate and the returns based on the decisions made are sometimes hard to determine. The developed game rules model such a situation, providing a Superintendent with a scenario to control cash flow for a theoretical site and contract. The game output will provide a data set to review the Superintendent’s performance in managing the cash flow presented in the game. Further research will use the game to study individual players and compare the results

EFFECTIVENESS OF LOW-COST CUSTOMIZED SADDLE PILLOW ON PAIN IN POST-EPISIOTOMY PATIENTS

Objective: To examine the effectiveness of customized saddle pillow for pain in post-episiotomy patients and also to analyze the duration of sitting for breastfeeding and other functional activities following episiotomy.Methods: A total of 28 postnatal mothers who have undergone episiotomy were included in the study based on the inclusion criteria and were divided conveniently into an experimental group (n=16) and control group (n=12). Both the groups received the conventional physiotherapy protocol, but experimental group patients, in addition, were provided with customized saddle pillow. Customized saddle pillow was used by the patients from postnatal day (PND) 0 to PND 2. Pre- and post-test values for pain were assessed through the numerical pain rating scale (NPRS). In addition, data such as duration of sitting for breastfeeding and other functional activities were collected through sitting tracker.Results: The study manifested the effectiveness of low-cost customized saddle pillow in reducing perineal pain (p=0.01) and increase in sitting duration (p=0.01) in post-episiotomy patients compared to the control group.Conclusion: Among the postnatal mothers selected for the study the mothers who used customized saddle pillow experienced a reduction in pain as well as the better sitting duration for breastfeeding. The research recommends mothers who underwent episiotomy to use the low-cost saddle pillows for healthier breastfeeding and pain-free life

Intercontinental spread of pyrimethamine-resistant malaria.

Here we present molecular evidence demonstrating that malaria parasites bearing high-level pyrimethamine resistance originally arrived in Africa from southeast Asia. The resistance alleles carried by these migrants are now spreading across Africa at an alarming rate, signaling the end of affordable malaria treatment and presenting sub-Saharan Africa with a public health crisis

Mechanism of Mg 2+ -accompanied product release in sugar nucleotidyltransferases

The nucleotidyl transfer reaction, catalyzed by sugar nucleotidyltransferases (SNTs), is assisted by two active site Mg 2+ ions. While studying this reaction using X-ray crystallography, we captured snapshots of the pyrophosphate (product) as it exits along a pocket. Surprisingly, one of the active site Mg 2+ ions remains coordinated to the exiting pyrophosphate. This hints at the participation of Mg 2+ in the process of product release, besides its role in catalyzing nucleotidyl transfer. These observations are further supported by enhanced sampling molecular dynamics simulations. Free energy computations suggest that the product release is likely to be rate limiting in SNTs, and the origin of the high free energy barrier for product release could be traced back to the “slow” conformational change of an Arg residue at the exit end of the pocket. These results establish a dual role for Mg 2+, and propose a general mechanism of product release during the nucleotidyl transfer by SNTs

Close kinship within multiple-genotype malaria parasite infections

Malaria infections containing multiple parasite genotypes are ubiquitous in nature, and play a central role in models of recombination, intra-host dynamics, virulence, sex ratio, immunity and drug resistance evolution in Plasmodium. While these multiple infections (MIs) are often assumed to result from superinfection (bites from multiple infected mosquitoes), we know remarkably little about their composition or generation. We isolated 336 parasite clones from eight patients from Malawi (high transmission) and six from Thailand (low transmission) by dilution cloning. These were genotyped using 384 single-nucleotide polymorphisms, revealing 22 independent haplotypes in Malawi (2–6 per MI) and 15 in Thailand (2–5 per MI). Surprisingly, all six patients from Thailand and six of eight from Malawi contained related haplotypes, and haplotypes were more similar within- than between-infections. These results argue against a simple superinfection model. Instead, the observed kinship patterns may be explained by inoculation of multiple related haploid sporozoites from single mosquito bites, by immune suppression of parasite subpopulations within infections, and serial transmission of related parasites between people. That relatedness is maintained in endemic areas in the face of repeated bites from infected mosquitoes has profound implications for understanding malaria transmission, immunity and intra-host dynamics of co-infecting parasite genotypes

Inferred relatedness and heritability in malaria parasites

Malaria parasites vary in phenotypic traits of biomedical or biological interest such as growth rate, virulence, sex ratio and drug resistance, and there is considerable interest in identifying the genes that underlie this variation. An important first step is to determine trait heritability (H2). We evaluate two approaches to measuring H2 in natural parasite populations using relatedness inferred from genetic marker data. We collected single-clone Plasmodium falciparum infections from 185 patients from the Thailand–Burma border, monitored parasite clearance following treatment with artemisinin combination therapy (ACT), measured resistance to six antimalarial drugs and genotyped parasites using 335 microsatellites. We found strong relatedness structure. There were 27 groups of two to eight clonally identical (CI) parasites, and 74 per cent of parasites showed significant relatedness to one or more other parasites. Initially, we used matrices of allele sharing and variance components (VC) methods to estimate H2. Inhibitory concentrations (IC50) for six drugs showed significant H2 (0.24 to 0.79, p = 0.06 to 2.85 × 10−9), demonstrating that this study design has adequate power. However, a phenotype of current interest—parasite clearance following ACT—showed no detectable heritability (H2 = 0–0.09, ns) in this population. The existence of CI parasites allows the use of a simple ANOVA approach for quantifying H2, analogous to that used in human twin studies. This gave similar results to the VC method and requires considerably less genotyping information. We conclude (i) that H2 can be effectively measured in malaria parasite populations using minimal genotype data, allowing rational design of genome-wide association studies; and (ii) while drug response (IC50) shows significant H2, parasite clearance following ACT was not heritable in the population studied