Molecular dynamics simulations of elementary chemical processes in liquid water using combined density functional and molecular mechanics potentials. I. Proton transfer in strongly H-bonded complexes

The first molecular dynamics (MD) simulation of a chemical process in solution with an ab initio description of the reactant species and a classical representation of the solvent is presented. We study the dynamics of proton (deuterium) transfer in strongly hydrogen-bonded systems characterized by an energy surface presenting a double well separated by a low activation barrier. We have chosen the hydroxyl-water complex in liquid water to analyze the coupling between the reactive system and the environment. The proton is transferred from one well to the other with a frequency close to 1 ps−1 which is comparable to the low-frequency band associated to hindered translations, diffusional translation and reorientation of water molecules in water. The proton transfer takes place in 20–30 fs whereas the solvent response is delayed by about 50 fs. Therefore, the reaction occurs in an essentially frozen-solvent configuration. In principle, this would produce a barrier increase with respect to the equilibrium reaction path. However, solvent fluctuations play a substantial role by catalyzing the proton transfer. The solvent relaxation time after proton transfer has been evaluated. Since it falls in the same time scale than the reactive events (0.6 ps) it substantially influences the proton dynamics. The present study is intended to model charge transfer processes in polar media having a low activation barrier for which many reactive events may be predicted in a MD simulation. The case of reactions with large activation barriers would require the use of special techniques to simulate rare events. But still in that case, hybrid QM/MM simulations represent a suitable tool to analyze reaction dynamics and non-equilibrium solvent effects in solution [email protected]

Feeling Tired?: How Sharing Positive Experiences Can Boost Vitality

Three studies indicated how sharing positive experiences can boost vitality

Molecular dynamics simulations of elementary chemical processes in liquid water using combined density functional and molecular mechanics potentials. II. Charge separation processes

A new approach to carry out molecular dynamics simulations of chemical reactions in solution using combined density functional theory/molecular mechanics potentials is presented. We focus our attention on the analysis of reactive trajectories, dynamic solvent effects and transmission coefficient rather than on the evaluation of free energy which is another important topic that will be examined elsewhere. In a previous paper we have described the generalities of this hybrid molecular dynamics method and it has been employed to investigate low energy barrier proton transfer process in water. The study of processes with activation energies larger than a few kT requires the use of specific techniques adapted to “rare events” simulations. We describe here a method that consists in the simulation of short trajectories starting from an equilibrated transition state in solution, the structure of which has been approximately established. This calculation is particularly efficient when carried out with parallel computers since the study of a reactive process is decomposed in a set of short time trajectories that are completely independent. The procedure is close to that used by other authors in the context of classical molecular dynamics but present the advantage of describing the chemical system with rigorous quantum mechanical calculations. It is illustrated through the study of the first reaction step in electrophilic bromination of ethylene in water. This elementary process is representative of many charge separation reactions for which static and dynamic solvent effects play a fundamental [email protected]

How prisoners and their partners experience the maintenance of their relationship during a prison sentence

Research shows that intimate relationships, and their maintenance via prison visits, have a positive impact on factors associated with prisoner well‐being and reduced likelihood of recidivism. It is therefore in the interest of corrections, government, and wider society to enable prisoners to maintain healthy relationships with their family and intimate partners throughout their prison sentence. Despite this evidence, little is known about how prisoners experience the maintenance of a significant intimate relationship in prison. This study aims to explore heterosexual couples' experiences in maintaining their well‐established intimate relationships, while the male partner is incarcerated. Four main themes were identified: how they experienced “having a special connection” that they were motivated to maintain; “coping with challenges and threats” to that connection; “developing reciprocal behaviours” to meet those challenges; and “maintaining a belief in the future.” Implications for how the relational context of rehabilitation can best be supported is considered

Exploring drivers of within-field crop yield variation using a national precision yield network

1. While abiotic drivers of yields represent important limiting factors to crop productivity, the role of biotic drivers that could be directly managed by farmers (e.g. agri-environment schemes supporting key ecosystem services) remains poorly understood. Precision yield mapping provides an opportunity to understand the factors that limit agricultural yield through the interpretation of high-resolution cropping data. This has the potential to inform future precision agricultural management, such as the targeted application of agrochemicals, promoting increased sustainability in modern agricultural systems. 2. We used precision yield measurements from a network of 1174 fields in England (2006–2020) to identify drivers of within-field yield variation in winter wheat and oilseed rape. Potential drivers included climate, topography and landscape composition and configuration. We then explored relationships between in-field yield patterns and local landscape context, including the presence of features associated with ecosystem benefits. 3. Proximity to the field edge was associated with reduced yields in 85% of wheat and 87% of oilseed fields. This translating to an approximate reduction of 10% in wheat and 18% in oilseed yields lost due to field edge effects. 4. We found evidence that reduced yields at the field edges were associated with biotic features of the surrounding landscape, including the occurrence of semi-natural habitats. Specifically, agri-environment scheme (AES) presence increased the rate at which yields at field edges approach those of the field centres. This suggests that AES occurrence within a landscape (rather than field adjacent) may increase edge effects. However, these trends are unclear and suggest interactions between drivers and the spatial and temporal scale of investigation. 5. Synthesis and applications. While we found evidence of landscape context mitigating against field edge effects, these were counterintuitive. For example, AES at a landscape scale appeared to increase the severity of edge effects. This study highlights a lack of environmental data at sufficiently high spatiotemporal resolution to match that of precision agriculture data. This mismatch is hindering the effective integration of precision agriculture data in an environmental policy and/or management context and potentially leading to unnecessarily poorly informed decisions related to AES deployment. This may limit environmental and economic benefits

A randomised controlled feasibility trial of music-assisted language telehealth intervention for minimally verbal autistic children-the MAP study protocol.

BACKGROUND: About 30% of children with autism spectrum disorder (ASD) do not develop functional speech and remain non-verbal or minimally verbal even after years of speech, language and educational interventions. A wide range of interventions have been developed for improving communication in ASD, but none have proved effective in eliciting functional language in ASD children. Research has found that people with ASD are more likely to have perfect pitch and prefer music to language. Further, it seems that language delay tends to co-occur with better musical skills. Brain imaging research has found that music alongside words increases the attention that people with ASD pay to spoken words. METHODS: In this protocol, we describe our music-assisted programmes (MAP) that will use music to attract the attention of people with ASD to speech. MAP may open the brain pathways to language and therefore help improve communication skills for people with ASD more than standard communication protocols. In particular, we aim to develop and test whether individualised, easily used MAP would increase spoken language in 24-60-month-old, nonverbal or minimally verbal children with ASD. We will develop a structured training method, delivered through naturalistic, interactive activities (e.g. songs) to teach language to ASD children. We will test this by comparing two groups: one undertaking music-assisted programmes, and the other receiving speech and language therapy in the way that is recommended in NHS clinics. Participants will be allocated to groups randomly. The feasibility of MAP will be assessed through estimations of recruitment and retention rates, the sensitivity and reliability of the outcome measures, the intensity and frequency of the trial, the usability of the MAP app (beta version), and the burden of the assessments for the children and parents. DISCUSSION: This feasibility randomised controlled trial will establish the acceptability and estimate the power of the MAP intervention to improve early word learning in children with ASD. In the longer term, this research will help us develop an app for parents or carers of children with ASD to design their own songs and implement their own individualised MAP. TRIAL REGISTRATION: ISRCTN, ISRCTN12536062 . Registered on 26 June 2019

Amelogenin Nanoparticles in Suspension: Deviations from Spherical Shape and pH-Dependent Aggregation

It is well-known that amelogenin self-assembles to form nanoparticles, usually referred to as amelogenin nanospheres, despite the fact that not much is known about their actual shape in solution. In the current paper, we combine SAXS and DLS to study the three-dimensional shape of the recombinant amelogenins rP172 and rM179. Our results show for the first time that amelogenins build oblate nanoparticles in suspension using experimental approaches that do not require the proteins to be in contact with a support material surface. The SAXS studies give evidence for the existence of isolated amelogenin nano-oblates with aspect ratios in the range of 0.45-0.5 at pH values higher than pH 7.2 and show an aggregation of these nano-oblates at lower pH values. The role of the observed oblate shape in the formation of chain-like structures at physiological conditions is discussed as a key factor in the biomineralization of dental enamel

Hydrodynamic interactions in colloidal ferrofluids: A lattice Boltzmann study

We use lattice Boltzmann simulations, in conjunction with Ewald summation methods, to investigate the role of hydrodynamic interactions in colloidal suspensions of dipolar particles, such as ferrofluids. Our work addresses volume fractions $\phi$ of up to 0.20 and dimensionless dipolar interaction parameters $\lambda$ of up to 8. We compare quantitatively with Brownian dynamics simulations, in which many-body hydrodynamic interactions are absent. Monte Carlo data are also used to check the accuracy of static properties measured with the lattice Boltzmann technique. At equilibrium, hydrodynamic interactions slow down both the long-time and the short-time decays of the intermediate scattering function $S(q,t)$, for wavevectors close to the peak of the static structure factor $S(q)$, by a factor of roughly two. The long-time slowing is diminished at high interaction strengths whereas the short-time slowing (quantified via the hydrodynamic factor $H(q)$) is less affected by the dipolar interactions, despite their strong effect on the pair distribution function arising from cluster formation. Cluster formation is also studied in transient data following a quench from $\lambda = 0$; hydrodynamic interactions slow the formation rate, again by a factor of roughly two

One-Step Purification of Recombinant Human Amelogenin and Use of Amelogenin as a Fusion Partner

Amelogenin is an extracellular protein first identified as a matrix component important for formation of dental enamel during tooth development. Lately, amelogenin has also been found to have positive effects on clinical important areas, such as treatment of periodontal defects, wound healing, and bone regeneration. Here we present a simple method for purification of recombinant human amelogenin expressed in Escherichia coli, based on the solubility properties of amelogenin. The method combines cell lysis with recovery/purification of the protein and generates a >95% pure amelogenin in one step using intact harvested cells as starting material. By using amelogenin as a fusion partner we could further demonstrate that the same method also be can explored to purify other target proteins/peptides in an effective manner. For instance, a fusion between the clinically used protein PTH (parathyroid hormone) and amelogenin was successfully expressed and purified, and the amelogenin part could be removed from PTH by using a site-specific protease