Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Too Many Materials and Too Many Applications: An Experimental Problem Waiting for a Computational Solution.

ABSTRACT: Finding the best material for a specific application is the ultimate goal of materials discovery. However, there is also the reverse problem: when experimental groups discover a new material, they would like to know all the possible applications this material would be promising for. Computational modeling can aim to fulfill this expectation, thanks to the sustained growth of computing power and the collective engagement of the scientific community in developing more efficient and accurate workflows for predicting materials' performances. We discuss the impact that reproducibility and automation of the modeling protocols have on the field of gas adsorption in nanoporous crystals. We envision a platform that combines these tools and enables effective matching between promising materials and industrial applications.

SUBMITTER: Ongari D

PROVIDER: S-EPMC7706098 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Too Many Materials and Too Many Applications: An Experimental Problem Waiting for a Computational Solution.

Ongari Daniele D Talirz Leopold L Smit Berend B

ACS central science 20201002 11

Finding the best material for a specific application is the ultimate goal of materials discovery. However, there is also the reverse problem: when experimental groups discover a new material, they would like to know all the possible applications this material would be promising for. Computational modeling can aim to fulfill this expectation, thanks to the sustained growth of computing power and the collective engagement of the scientific community in developing more efficient and accurate workfl ...[more]

PMID: 33274268

Similar Datasets

Computational Investigations on Soundproof Applications of Foam-Formed Cellulose Materials.

Project description:Recent studies have highlighted an innovative way to produce highly porous materials based on cellulose fibers. These studies have focused on the foam-forming process, where the cellulose fibers and other components are mixed with foam. In the authors' previous research, the foam-formed cellulose materials (FCM) were obtained by mixing a surfactant with cellulose fibers, taken from virgin pulp and recovered papers. In the present paper, the authors performed additional experimental and computational analyses in order to evaluate the sound insulation capabilities of these FCM beyond the initial impedance of tube investigations. The poroacoustics computational methodology parameters-i.e., airflow resistivity, porosity, tortuosity, viscous, and thermal characteristic lengths-were herein evaluated. This analysis was performed using both a theoretical/empirical approach from the specialized literature and an experimental investigation developed by the authors. The computational investigations were conducted in two stages: First, we evaluated the approximation of the experimentally gained normal incidence parameters, in terms of absorption and reflection, respectively, relative to the estimated ones. The second stage of analysis consists of a parametrical estimation of sound insulation characteristics concerning the incidence angle of sound hitting the porous layer. The results presented in this paper are in agreement with the computational experimental results, providing extended soundproof characteristics to the incidence angle of the acoustic field. Further, this study supplies additional information useful for future analyses regarding the influences of random geometry air inclusions into the FCM layer.

| S-EPMC6680988 | biostudies-literature

A Solution to the Common Problem of the Synthesis and Applications of Hexachlorofluorescein Labeled Oligonucleotides.

Project description:A common problem of the preparation of hexachlorofluorescein labeled oligonucleotides is the transformation of the fluorophore to an arylacridine derivative under standard ammonolysis conditions. We show here that the arylacridine byproduct with distinct optical characteristics cannot be efficiently separated from the major product by HPLC or electrophoretic methods, which hampers precise physicochemical experiments with the labeled oligonucleotides. Studies of the transformation mechanism allowed us to select optimal conditions for avoiding the side reaction. The novel method for the post-synthetic deblocking of hexachlorofluorescein-labeled oligodeoxyribonucleotides described in this paper prevents the formation of the arylacridine derivative, enhances the yield of target oligomers, and allows them to be proper real-time PCR probes.

| S-EPMC5115841 | biostudies-literature

Studying the evolution of promoter sequences: a waiting time problem.

Project description:To gain a better understanding of the evolutionary dynamics of regulatory DNA sequences, we address the following questions: (1) How long does it take until a given transcription factor (TF) binding site emerges at random in a promoter sequence? and (2) How does the composition of a TF binding site affect this waiting time? Using two different probabilistic models (an i.i.d. model and a neighbor dependent model), we can compute the expected waiting time for every k-mer, k ranging from 5 to 10, until it appears in a promoter of a species. Our findings indicate that new TF binding sites can be created on a short evolutionary time scale, i.e. in a time span below the speciation time of human and chimp. Furthermore, one can conclude that the composition of a TF binding site plays a crucial role concerning the waiting time until it appears and that the CpG methylation-deamination substitution process probably accelerates the creation of new TF binding sites. A screening of existing TF binding sites moreover reveals that k-mers predicted to have short waiting times occur more frequently than others. Supplementary Material is available at www.libertonline.com/cmb .

| S-EPMC3119604 | biostudies-literature

Experimental and Computational Hydrate Screening: Cytosine, 5-Flucytosine and Their Solid Solution.

Project description:The structural, temperature- and moisture dependent stability features of cytosine and 5-flucytosine monohydrates, two pharmaceutically important compounds, were rationalized using complementary experimental and computational approaches. Moisture sorption/desorption, water activity, thermal analysis and calorimetry were applied to determine the stability ranges of hydrate ↔ anhydrate systems, while X-ray diffraction, IR spectroscopy and crystal structure prediction provided the molecular level understanding. At 25 °C, the critical water activity for the cytosine hydrate ↔ anhydrate system is ~0.43 and for 5-flucytosine ~0.41. In 5-flucytosine the water molecules are arranged in open channels, therefore the kinetic desorption data, dehydration < 40% relative humidity (RH), conform with the thermodynamic data, whereas for the cytosine isolated site hydrate dehydration was observed at RH < 15%. Peritectic dissociation temperatures of the hydrates were measured to be 97 °C and 84.2 °C for cytosine and 5-flucytosine, respectively, and the monohydrate to anhydrate transition enthalpies to be around 10 kJ mol-1. Computed crystal energy landscapes not only revealed that the substitution of C5 (H or F) controls the packing and properties of cytosine/5-flucytosine solid forms, but also have enabled the finding of a monohydrate solid solution of the two substances which shows increased thermal- and moisture-dependent stability compared to 5-flucytosine monohydrate.

| S-EPMC6193535 | biostudies-literature

Thermodynamics of Hydrophobic Amino Acids in Solution: A Combined Experimental-Computational Study.

Project description:We present a joint experimental-computational study to quantitatively describe the thermodynamics of hydrophobic leucine amino acids in aqueous solution. X-ray scattering data were acquired at a series of solute and salt concentrations to effectively measure interleucine interactions, indicating that a major scattering peak is observed consistently at q = 0.83 Å-1. Atomistic molecular dynamics simulations were then performed and compared with the scattering data, achieving high consistency at both small and wider scattering angles (q = 0-1.5 Å-1). This experimental-computational consistence enables a first glimpse of the leucine-leucine interacting landscape, where two leucine molecules are aligned mostly in a parallel fashion, as opposed to antiparallel, but also allows us to derive effective leucine-leucine interactions in solution. Collectively, this combined approach of employing experimental scattering and molecular simulation enables quantitative characterization of effective intermolecular interactions of hydrophobic amino acids, critical for protein function and dynamics such as protein folding.

| S-EPMC5256481 | biostudies-literature

The many weak instruments problem and Mendelian randomization.

Project description:Instrumental variable estimates of causal effects can be biased when using many instruments that are only weakly associated with the exposure. We describe several techniques to reduce this bias and estimate corrected standard errors. We present our findings using a simulation study and an empirical application. For the latter, we estimate the effect of height on lung function, using genetic variants as instruments for height. Our simulation study demonstrates that, using many weak individual variants, two-stage least squares (2SLS) is biased, whereas the limited information maximum likelihood (LIML) and the continuously updating estimator (CUE) are unbiased and have accurate rejection frequencies when standard errors are corrected for the presence of many weak instruments. Our illustrative empirical example uses data on 3631 children from England. We used 180 genetic variants as instruments and compared conventional ordinary least squares estimates with results for the 2SLS, LIML, and CUE instrumental variable estimators using the individual height variants. We further compare these with instrumental variable estimates using an unweighted or weighted allele score as single instruments. In conclusion, the allele scores and CUE gave consistent estimates of the causal effect. In our empirical example, estimates using the allele score were more efficient. CUE with corrected standard errors, however, provides a useful additional statistical tool in applications with many weak instruments. The CUE may be preferred over an allele score if the population weights for the allele score are unknown or when the causal effects of multiple risk factors are estimated jointly.

| S-EPMC4305205 | biostudies-literature

Stem cell differentiation as a many-body problem.

Project description:Stem cell differentiation has been viewed as coming from transitions between attractors on an epigenetic landscape that governs the dynamics of a regulatory network involving many genes. Rigorous definition of such a landscape is made possible by the realization that gene regulation is stochastic, owing to the small copy number of the transcription factors that regulate gene expression and because of the single-molecule nature of the gene itself. We develop an approximation that allows the quantitative construction of the epigenetic landscape for large realistic model networks. Applying this approach to the network for embryonic stem cell development explains many experimental observations, including the heterogeneous distribution of the transcription factor Nanog and its role in safeguarding the stem cell pluripotency, which can be understood by finding stable steady-state attractors and the most probable transition paths between those attractors. We also demonstrate that the switching rate between attractors can be significantly influenced by the gene expression noise arising from the fluctuations of DNA occupancy when binding to a specific DNA site is slow.

| S-EPMC4104876 | biostudies-literature

The computational capabilities of many-to-many protein interaction networks.

Project description:Many biological circuits comprise sets of protein variants that interact with one another in a many-to-many, or promiscuous, fashion. These architectures can provide powerful computational capabilities that are especially critical in multicellular organisms. Understanding the principles of biochemical computations in these circuits could allow more precise control of cellular behaviors. However, these systems are inherently difficult to analyze, due to their large number of interacting molecular components, partial redundancies, and cell context dependence. Here, we discuss recent experimental and theoretical advances that are beginning to reveal how promiscuous circuits compute, what roles those computations play in natural biological contexts, and how promiscuous architectures can be applied for the design of synthetic multicellular behaviors.

| S-EPMC10318606 | biostudies-literature

A many-objective evolutionary algorithm based on three states for solving many-objective optimization problem.

Project description:In recent years, researchers have taken the many-objective optimization algorithm, which can optimize 5, 8, 10, 15, 20 objective functions simultaneously, as a new research topic. However, the current research on many-objective optimization technology also encounters some challenges. For example: Pareto resistance phenomenon, difficult diversity maintenance. Based on the above problems, this paper proposes a many-objective evolutionary algorithm based on three states (MOEA/TS). Firstly, a feature extraction operator is proposed. It can extract the features of the high-quality solution set, and then assist the evolution of the current individual. Secondly, based on Pareto front layer, the concept of "individual importance degree" is proposed. The importance degree of an individual can reflect the importance of the individual in the same Pareto front layer, so as to further distinguish the advantages and disadvantages of different individuals in the same front layer. Then, a repulsion field method is proposed. The diversity of the population in the objective space is maintained by the repulsion field, so that the population can be evenly distributed on the real Pareto front. Finally, a new concurrent algorithm framework is designed. In the algorithm framework, the algorithm is divided into three states, and each state focuses on a specific task. The population can switch freely among these three states according to its own evolution. The MOEA/TS algorithm is compared with 7 advanced many-objective optimization algorithms. The experimental results show that the MOEA/TS algorithm is more competitive in many-objective optimization problems.

| S-EPMC11333576 | biostudies-literature

Synthesis of Macromolecular Aromatic Epoxy Resins as Anticorrosive Materials: Computational Modeling Reinforced Experimental Studies.

Project description:Herein, two bifunctional macromolecular aromatic epoxy resins (ERs), namely, 4,4'-isopropylidenediphenol oxirane (ERH) and 4,4'-isopropylidene tetrabromodiphenol oxirane (ERBr), are synthesized, characterized, and evaluated as anticorrosive materials for carbon steel corrosion in acidic medium. ERs were characterized using proton nuclear magnetic resonance (1H NMR) and Fourier transform infrared spectroscopy techniques. Investigated ERs acted as effective corrosion inhibitors, and their inhibition effectiveness followed the order ERBr (96.5%) > ERH (95.6%). Potentiodynamic polarization results showed that ERH and ERBr behave as predominantly anodic type and the cathodic type of corrosion inhibitors, respectively. Adsorption of both the studied ERH and ERBr molecules obeyed the Langmuir adsorption isotherm model. Density functional theory and molecular dynamics studies showed that protonated forms of ERH and ERBr contribute more to metal (carbon steel)-inhibitor (ERH/ERBr) interactions than their neutral forms.

| S-EPMC7045322 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data