Large scale simulations of a detailed molecular model of seawater: Ionic conductivity and diffusion coefficients of CO2.

Oceans are essentially an electrolyte solution. The experimental study of physical and chemical processes occurring in oceans remains challenging, so molecular dynamics simulations may be of great help. We have recently demonstrated that simulations using a state-of-the-art force field can accurately describe the thermophysical properties of seawater by employing a detailed chemical model of the solution.

Solid-Liquid Interfacial Free Energy from Computer Simulations: Challenges and Recent Advances.

The study of interfacial properties in liquid-liquid and liquid-vapor systems has a history of nearly 200 years, with significant contributions from scientific luminaries such as Thomas Young and Willard Gibbs. However, a similar level of understanding of solid-liquid interfaces has emerged only more recently, largely because of the numerous complications associated with the thermodynamics needed to describe them. The accurate calculation of the interfacial free energy of solid-liquid systems is central to determining which interfaces will be observed and their properties.

Optimizing optical coherence tomography to detect occult spermatozoa in rat testis after induced non-obstructive azoospermia.

Significance: The ability to detect and localize sperm in the testes is crucial for the treatment of non-obstructive azoospermia (NOA), a condition where sperm retrieval is challenging due to the lack of visible sperm. Enhancing the accuracy and efficiency of sperm detection can significantly improve the outcomes of microdissection testicular sperm extraction (micro-TESE) procedures in NOA patients.

Aim: We aim to use optical coherence tomography (OCT) to detect the presence or absence of sperm in the imaged areas of the testes and to localize sperm-containing seminiferous tubules in a rat model of NOA.

TIP 4 P 2005 Ice : Simulating water with two molecular states.

Rigid, non-polarizable water models are very efficient from a computational point of view, and some of them have a great ability in predicting experimental properties. There is, however, little room for improvement in simulating water with this strategy, whose main shortcoming is that water molecules do not change their interaction parameters in response to the local molecular landscape. In this work, we propose a novel modeling strategy that involves using two rigid non-polarizable models as states that water molecules can adopt depending on their molecular environment.

Feasibility study of hyperspectral colposcopy as a novel tool for detecting precancerous cervical lesions.

Cervical cancer remains a major global health concern, with a specially alarming incidence in younger women. Traditional detection techniques such as the Pap smear and colposcopy often lack sensitivity and specificity and are highly dependent on the experience of the gynaecologist. In response, this study proposes the use of Hyperspectral Imaging, a pioneering technology that combines traditional imaging with spectroscopy to provide detailed spatial and spectral information.

On the compatibility of the Madrid-2019 force field for electrolytes with the TIP4P/Ice water model.

The Madrid-2019 force field was recently developed to perform simulations of electrolytes in water. The model was specifically parameterized for TIP4P/2005 water and uses scaled charges for the ions. In this work, we test the compatibility of the Madrid-2019 force field with another water model: TIP4P/Ice.

Predictions of the interfacial free energy along the coexistence line from single-state calculations.

The calculation of the interfacial free energy between two thermodynamic phases is crucial across various fields, including materials science, chemistry, and condensed matter physics. In this study, we apply an existing thermodynamic approach, the Gibbs-Cahn integration method, to determine the interfacial free energy under different coexistence conditions, relying on data from a single-state calculation at specified pressure and temperature. This approach developed by Laird et al.

Strong Correlation Between Double-Strand DNA Breaks and Total Sperm DNA Fragmentation in the Human Ejaculate.

Background: Double- and single-strand DNA breaks (DSBs and SSBs, respectively) in spermatozoa, which emerge from intrinsic and extrinsic degenerative processes, are likely related to the underlying male pathology.

Aim: To determine whether the incidence of DSBs in the human ejaculate is a consistent predictor of whole sperm DNA fragmentation (W-SDF = SSBs + DSBs).

Methods: A correlation between the proportion of spermatozoa that showed whole W-SDF and those displaying only DSBs in DNA.

Statistical mechanics of crystal nuclei of hard spheres.

In the study of crystal nucleation via computer simulations, hard spheres are arguably the most extensively explored model system. Nonetheless, even in this simple model system, the complex thermodynamics of crystal nuclei can sometimes give rise to counterintuitive results, such as the recent observation that the pressure inside a critical nucleus is lower than that of the surrounding fluid, seemingly clashing with the strictly positive Young-Laplace pressure we would expect in liquid droplets. Here, we re-derive many of the founding equations associated with crystal nucleation and use the hard-sphere model to demonstrate how they give rise to this negative pressure difference.

Dressing a Nonpolarizable Force Field for OH in TIP4P/2005 Aqueous Solutions with Corrected Hirshfeld Charges.

We present a rigid model for the OH ion parametrized for binary mixtures with TIP4P/2005-type water molecules. Li, Na and K were selected as counterions, hence mimicking the important and widely used solutions of soluble alkaline hydroxides. The optimized atomic charge distributions were obtained by scaling in a factor of 0.

Antiparasitic Evaluation of Aquiluscidin, a Cathelicidin Obtained from , and the Vcn-23 Derivative Peptide against , and .

Babesiosis is a growing concern due to the increased prevalence of this infectious disease caused by protozoan parasites, affecting various animals and humans. With rising worries over medication side effects and emerging drug resistance, there is a notable shift towards researching babesiacidal agents. Antimicrobial peptides, specifically cathelicidins known for their broad-spectrum activity and immunomodulatory functions, have emerged as potential candidates.

Variational umbrella seeding for calculating nucleation barriers.

In this work, we introduce variational umbrella seeding, a novel technique for computing nucleation barriers. This new method, a refinement of the original seeding approach, is far less sensitive to the choice of order parameter for measuring the size of a nucleus. Consequently, it surpasses seeding in accuracy and umbrella sampling in computational speed.

Accurate Free Energies of Aqueous Electrolyte Solutions from Molecular Simulations with Non-polarizable Force Fields.

Non-polarizable force fields fail to accurately predict free energies of aqueous electrolytes without compromising the predictive ability for densities and transport properties. A new approach is presented in which (1) TIP4P/2005 water and scaled charge force fields are used to describe the interactions in the liquid phase and (2) an additional Effective Charge Surface (ECS) is used to compute free energies at zero additional computational expense. The ECS is obtained using a single temperature-independent charge scaling parameter per species.

BioKC: a collaborative platform for curation and annotation of molecular interactions.

Curation of biomedical knowledge into systems biology diagrammatic or computational models is essential for studying complex biological processes. However, systems-level curation is a laborious manual process, especially when facing ever-increasing growth of domain literature. New findings demonstrating elaborate relationships between multiple molecules, pathways and cells have to be represented in a format suitable for systems biology applications.

Urticaria Pigmentosa Without Pruritus.

Mastocytosis is a group of disorders characterized by the pathologic accumulation of mast cells in various tissues. One example of mastocytosis is urticaria pigmentosa, which presents with mastocytomas that can cause hives and, when irritated, pruritus. To our knowledge, we are describing the first case of urticaria pigmentosa without pruritus.

Programme Dementia Prevention (pdp): A Nationwide Program for Personalized Prevention in Luxembourg.

Background: With continuously aging societies, an increase in the number of people with cognitive decline is to be expected. Aside from the development of causative treatments, the successful implementation of prevention strategies is of utmost importance to reduce the high societal burden caused by neurodegenerative diseases leading to dementia among which the most common cause is Alzheimer's disease.

Objective: The aim of the Luxembourgish "programme dementia prevention (pdp)" is to prevent or at least delay dementia in an at-risk population through personalized multi-domain lifestyle interventions.

Further extension of the Madrid-2019 force field: Parametrization of nitrate (NO3-) and ammonium (NH4+) ions.

The importance of nitrate and ammonium salts both in the environment and in biological processes cannot be questioned. In this work, using the TIP4P/2005 water model, aqueous solutions of nitrate and ammonium electrolytes are parametrized using scaled charges while keeping a rigid structure and nonpolarizable charge distributions. The models are optimized by systematically testing a set of properties for twelve electrolytes-eight nitrate and four ammonium salts-thus, enlarging the number of potential chemical species encompassed within the Madrid-2019 force field for ions.

Computation of Electrical Conductivities of Aqueous Electrolyte Solutions: Two Surfaces, One Property.

In this work, we computed electrical conductivities under ambient conditions of aqueous NaCl and KCl solutions by using the Einstein-Helfand equation. Common force fields (charge = ±1 ) do not reproduce the experimental values of electrical conductivities, viscosities, and diffusion coefficients. Recently, we proposed the idea of using different charges to describe the potential energy surface (PES) and the dipole moment surface (DMS).

On the possible locus of the liquid-liquid critical point in real water from studies of supercooled water using the TIP4P/Ice model.

One of the most accepted hypothesis to explain the anomalous behavior of water is the presence of a critical point between two liquids, the liquid-liquid critical point (LLCP), buried within the deep supercooled regime. Unfortunately, such hypothesis is hard to be experimentally confirmed due to fast freezing. Here, we show that the TIP4P/Ice water potential shifted by 400 bar can reproduce with unprecedented accuracy the experimental isothermal compressibility of water and its liquid equation of state for a wide pressure and temperature range.

Solubility of carbon dioxide in water: Some useful results for hydrate nucleation.

In this paper, the solubility of carbon dioxide (CO2) in water along the isobar of 400 bar is determined by computer simulations using the well-known TIP4P/Ice force field for water and the TraPPE model for CO2. In particular, the solubility of CO2 in water when in contact with the CO2 liquid phase and the solubility of CO2 in water when in contact with the hydrate have been determined. The solubility of CO2 in a liquid-liquid system decreases as the temperature increases.

The water cavitation line as predicted by the TIP4P/2005 model.

The formation of vapor bubbles in a metastable liquid, cavitation, is an activated process due to the free energy cost of having both phases at contact. Such an energetic penalty enables the existence of the liquid beyond its thermodynamic borders. Establishing the stability limits of a liquid as ubiquitous as water has important practical implications and has thereby attracted a lot of attention.

Estimation of bubble cavitation rates in a symmetrical Lennard-Jones mixture by NVT seeding simulations.

The liquid-vapor transition starts with the formation of a sufficiently large bubble in the metastable liquid to trigger the phase transition. Understanding this process is of fundamental and practical interest, but its study is challenging because it occurs over timescales that are too short for experiments but too long for simulations. The seeding method estimates cavitation rates by simulating a liquid in which a bubble is inserted, thus avoiding the long times needed for its formation.

Analysis: Flawed Datasets of Monkeypox Skin Images.

The self-proclaimed first publicly available dataset of Monkeypox skin images consists of medically irrelevant images extracted from Google and photography repositories through a process denominated web-scrapping. Yet, this did not stop other researchers from employing it to build Machine Learning (ML) solutions aimed at computer-aided diagnosis of Monkeypox and other viral infections presenting skin lesions. Neither did it stop the reviewers or editors from publishing these subsequent works in peer-reviewed journals.