Topology of thermodynamic potentials using physical models: Helmholtz, Gibbs, Grand, and Null.

Thermodynamic potentials play a substantial role in numerous scientific disciplines and serve as basic constructs for describing the behavior of matter. Despite their significance, comprehensive investigations of their topological characteristics and their connections to molecular interactions have eluded exploration due to experimental inaccessibility issues. This study addresses this gap by analyzing the topology of the Helmholtz energy, Gibbs energy, Grand potential, and Null potential that are associated with different isothermal boundary conditions.

Reasoning about actual causation in reversible and irreversible causal structures.

This article investigates people's judgments of actual causation in the context of a previously neglected property of causal structures-their reversibility, that is, whether an effect persists or returns to its original state if its causes are removed. Causal reversibility, and its potential impact on causal judgment, was recently analyzed theoretically by Ross and Woodward (2022). They hypothesized that reversibility might affect people's evaluation of causes in late-preemption scenarios.

Agent-based approaches for biological modeling in oncology: A literature review.

Context: Computational modeling involves the use of computer simulations and models to study and understand real-world phenomena. Its application is particularly relevant in the study of potential interactions between biological elements. It is a promising approach to understand complex biological processes and predict their behavior under various conditions.

Elucidating the behavior of the SARS-CoV-2 virus surface at vapor-liquid interfaces using molecular dynamics simulation.

Aerosols play a major role in the transmission of the SARS-CoV-2 virus. The behavior of the virus within aerosols is therefore of fundamental importance. On the surface of a SARS-CoV-2 virus, there are about 40 spike proteins, which each have a length of about 20 nm.

A child of prediction. On the History, Ontology, and Computation of the Lennard-Jonesium.

The Lennard-Jones (LJ) fluid, named after mathematician-physicist-chemist Sir John Lennard-Jones (1894-1954), occupies a special place among fluids. It is an ideal entity, defined as the fluid whose particles interact according to the Lennard-Jones potential. This paper expounds the history of the LJ fluid to throw light on the tensions between theory and computational practice.

Extension of the Database to Transferable Force Fields.

, a web-based database for classical force fields for molecular simulations of fluids [, 10 (), 806-814], was extended to transferable force fields. Eight transferable force fields, including all-atom and united-atom type force fields, were implemented in the database: OPLS-UA, OPLS-AA, COMPASS, CHARMM, GROMOS, TraPPE, Potoff, and TAMie. These transferable force fields cover a large variety of chemical substance classes.

Revisiting the narrow latent scope bias in explanatory reasoning.

Humans are capable explainers and lay people tend to share the same explanatory virtues held in high regard by philosophers and scientists. However, a recent line of studies found a striking deviation from normativity in lay people's explanations, termed the "narrow latent scope bias". When competing explanations with identical a priori probabilities fit observed evidence equally well - but differ in the number of unobserved pieces of evidence they predict (latent scope) - reasoners seem to prefer explanations that predict fewer unobserved pieces of evidence (narrow latent scope).

Molecular dynamics simulation study on the mass transfer across vapor-liquid interfaces in azeotropic mixtures.

Mass transfer through fluid interfaces is an important phenomenon in industrial applications as well as in naturally occurring processes. In this work, we investigate the mass transfer across vapor-liquid interfaces in binary mixtures using molecular dynamics simulations. We investigate the influence of interfacial properties on mass transfer by studying three binary azeotropic mixtures known to have different interfacial behaviors.

Data scheme and data format for transferable force fields for molecular simulation.

A generalized data scheme for transferable classical force fields used in molecular simulations, i.e. molecular dynamics and Monte Carlo simulation, is presented.

Phase equilibria of symmetric Lennard-Jones mixtures and a look at the transport properties near the upper critical solution temperature.

This study investigates phase equilibria and transport properties of five symmetric binary Lennard-Jones mixtures using molecular simulation and equation of state models. The mixtures are selected for their representation of different types of phase behavior and the research contributes to the development of simulation techniques, mixture theories and understanding of thermophysical mixture properties. A novel method is introduced for determining the critical end point (CEP) and critical azeotropic end point (CAEP) by molecular simulation.

Mass Transfer through Vapor-Liquid Interfaces Studied by Non-Stationary Molecular Dynamics Simulations.

Molecular dynamics (MD) simulations are highly attractive for studying the influence of interfacial effects, such as the enrichment of components, on the mass transfer through the interface. In a recent work, we have presented a steady-state MD simulation method for investigating this phenomenon and tested it using model mixtures with and without interfacial enrichment. The present study extends this work by introducing a non-stationary MD simulation method.

Determining Brown's Characteristic Curves Using Molecular Simulation.

Brown's characteristic curves define lines on the thermodynamic surface where special thermodynamic conditions hold. These curves are an important tool for the development of thermodynamic models of fluids. Yet, practically no experimental data for Brown's characteristic curves is available.

Comparison of Force Fields for the Prediction of Thermophysical Properties of Long Linear and Branched Alkanes.

The prediction of thermophysical properties at extreme conditions is an important application of molecular simulations. The quality of these predictions primarily depends on the quality of the employed force field. In this work, a systematic comparison of classical transferable force fields for the prediction of different thermophysical properties of alkanes at extreme conditions, as they are encountered in tribological applications, was carried out using molecular dynamics simulations.

The perceived dilution of causal strength.

Dependency theories of causal reasoning, such as causal Bayes net accounts, postulate that the strengths of individual causal links are independent of the causal structure in which they are embedded; they are inferred from dependency information, such as statistical regularities. We propose a psychological account that postulates that reasoners' concept of causality is richer. It predicts a systematic influence of causal structure knowledge on causal strength intuitions.

Interfacial properties of binary azeotropic mixtures of simple fluids: Molecular dynamics simulation and density gradient theory.

Interfacial properties of binary azeotropic mixtures of Lennard-Jones truncated and shifted fluids were studied by molecular dynamics (MD) simulation and density gradient theory (DGT) in combination with an equation of state. Three binary mixtures were investigated, which differ in the energetic cross interaction parameter that yields different types of azeotropic behavior. This study covers a wide temperature and composition range.

Conditionals and the hierarchy of causal queries.

Recent studies indicate that indicative conditionals like "If people wear masks, the spread of Covid-19 will be diminished" require a probabilistic dependency between their antecedents and consequents to be acceptable (Skovgaard-Olsen et al., 2016). But it is easy to make the slip from this claim to the thesis that indicative conditionals are acceptable only if this probabilistic dependency results from a causal relation between antecedent and consequent.

The role of mechanism knowledge in singular causation judgments.

Singular causation queries (e.g., "Did Mary's taking contraceptives cause her thrombosis?") are ubiquitous in everyday life and crucial in many professional disciplines, such as medicine or law.

A counterfactual simulation model of causation by omission.

When do people say that an event that did not happen was a cause? We extend the counterfactual simulation model (CSM) of causal judgment (Gerstenberg, Goodman, Lagnado, & Tenenbaum, 2021) and test it in a series of three experiments that look at people's causal judgments about omissions in dynamic physical interactions. The problem of omissive causation highlights a series of questions that need to be answered in order to give an adequate causal explanation of why something happened: what are the relevant variables, what are their possible values, how are putative causal relationships evaluated, and how is the causal responsibility for an outcome attributed to multiple causes? The CSM predicts that people make causal judgments about omissions in physical interactions by using their intuitive understanding of physics to mentally simulate what would have happened in relevant counterfactual situations. Prior work has argued that normative expectations affect judgments of omissive causation.

Molecular Dynamics Study of Wetting and Adsorption of Binary Mixtures of the Lennard-Jones Truncated and Shifted Fluid on a Planar Wall.

The wetting of surfaces is strongly influenced by adsorbate layers. Therefore, in this work, sessile drops and their interaction with adsorbate layers on surfaces were investigated by molecular dynamics simulations. Binary fluid model mixtures were considered.

Interpolating causal mechanisms: The paradox of knowing more.

Causal knowledge is not static; it is constantly modified based on new evidence. The present set of seven experiments explores 1 important case of causal belief revision that has been neglected in research so far: causal interpolations. A simple prototypic case of an interpolation is a situation in which we initially have knowledge about a causal relation or a positive covariation between 2 variables but later become interested in the mechanism linking these 2 variables.

Catheter-based Arterial Input Function Determination for Myocardial Perfusion Measurements.

The quantification of myocardial perfusion with contrast agent (CA) tracers requires the precise knowledge of the arterial input function (AIF). In this study a method for MR-guided vascular interventions is evaluated that determines the AIF via an active tracking catheter during targeted CA injection. A phantom experiment with a dialysis filter was conducted to measure the AIF using an active catheter and a dynamic image series as reference.

Characteristic Curves of the Lennard-Jones Fluid.

Equations of state based on intermolecular potentials are often developed about the Lennard-Jones (LJ) potential. Many of such EOS have been proposed in the past. In this work, 20 LJ EOS were examined regarding their performance on Brown's characteristic curves and characteristic state points.

Time and Singular Causation-A Computational Model.

Causal queries about singular cases, which inquire whether specific events were causally connected, are prevalent in daily life and important in professional disciplines such as the law, medicine, or engineering. Because causal links cannot be directly observed, singular causation judgments require an assessment of whether a co-occurrence of two events c and e was causal or simply coincidental. How can this decision be made? Building on previous work by Cheng and Novick (2005) and Stephan and Waldmann (2018), we propose a computational model that combines information about the causal strengths of the potential causes with information about their temporal relations to derive answers to singular causation queries.

Interfacial properties of binary mixtures of simple fluids and their relation to the phase diagram.

Interfacial properties of binary fluid mixtures were studied using both molecular dynamics (MD) simulations and density gradient theory (DGT). The focus of the study is on the relation of the interfacial properties to the phase diagram of the mixture. Two binary Lennard-Jones mixtures were investigated in a wide range of states: a highly asymmetric mixture (type III), which exhibits vapour-liquid equilibria (VLE and VLE), liquid-liquid equilibria (LLE), a three-phase equilibrium (VLLE), and supercritical fluid-fluid equilibria (FFE), and, as a reference, an ideal mixture (type I).

A Force Field for Poly(oxymethylene) Dimethyl Ethers (OME).

A united atom force field for the homologous series of the poly(oxymethylene) dimethyl ethers (OME), HC-O-(CHO)-CH, is presented. OME are oxygenates and promising new synthetic fuels and solvents. The molecular geometry of the OME, the internal degrees of freedom, and their electrostatic properties were obtained from quantum mechanical calculations.