It is difficult to relate the properties of liquids and glasses directly to their structure because of complexity in the structure that defies precise definition. The potential energy landscape (PEL) approach is a very insightful way to conceptualize the structure-property relationship in liquids and glasses, particularly the effect of temperature and history. However, because of the highly multidimensional nature of the PEL it is hard to determine, or even visualize, the actual details of the energy landscape. In this article we introduce a modified concept of the local energy landscape (LEL), which is limited in phase space, and demonstrate its usefulness using molecular dynamics simulation on a simple liquid at high temperatures. The local energy landscape is given as a function of the local coordination number, the number of the nearest-neighbor atoms. The excitation in the LEL corresponds to the so-called β-relaxation process. The LEL offers a simple but useful starting point to discuss complex phenomena in liquids and glasses.
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http://dx.doi.org/10.1103/PhysRevE.90.052307 | DOI Listing |
iScience
January 2025
Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece.
The genome of () DSM 2661 was the first Archaeal genome to be sequenced in 1996. Subsequent sequence-based annotation cycles led to its first metabolic reconstruction in 2005. Leveraging new experimental results and function assignments, we have now re-annotated creating an updated resource with novel information and testable predictions in a pathway-genome database available at BioCyc.
View Article and Find Full Text PDFMol Biol Evol
January 2025
Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France.
Allosteric regulation is a powerful mechanism for controlling the efficiency of enzymes. Deciphering the evolutionary mechanisms by which allosteric properties have been acquired in enzymes is of fundamental importance. We used the malate (MalDH) and lactate deydrogenases (LDHs) superfamily as model to elucidate this phenomenon.
View Article and Find Full Text PDFDalton Trans
January 2025
Chemistry Department, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland.
Stimulus-responsive molecular materials are highly desirable because of the wide range of their potential applications. In particular, switching of physical properties opens application pathways for molecular materials as sensors or actuators. Property switching in solids can be achieved by inducing single-crystal-to-single-crystal (SCSC) phase transitions.
View Article and Find Full Text PDFNew Phytol
January 2025
Department of Biological Sciences, Northern Arizona University, PO Box 5640, Flagstaff, 86011, AZ, USA.
Nat Commun
January 2025
Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
Enzyme engineering is limited by the challenge of rapidly generating and using large datasets of sequence-function relationships for predictive design. To address this challenge, we develop a machine learning (ML)-guided platform that integrates cell-free DNA assembly, cell-free gene expression, and functional assays to rapidly map fitness landscapes across protein sequence space and optimize enzymes for multiple, distinct chemical reactions. We apply this platform to engineer amide synthetases by evaluating substrate preference for 1217 enzyme variants in 10,953 unique reactions.
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