Prebiotic chemistry and origins of life research with atomistic computer simulations.

Research in origins of life is an intrinsically multi-disciplinary field, aimed at finding answers to the formidably complex problem of understanding the emergence of life from the modern versions of Charles Darwin's celebrated "primordial soup". In the last few years, thanks to the increasing computational power and the development of sophisticated theoretical and numerical methods, several computational chemistry and physics groups have invested this field, providing new microscopic insights on fundamental prebiotic chemistry phenomena possibly occurring in the early Earth and outer space. This review presents the most successful and powerful approaches in computational chemistry, and the main results thus obtained in prebiotic chemistry and origins of life.

Synthesis of RNA Nucleotides in Plausible Prebiotic Conditions from ab Initio Computer Simulations.

Understanding the mechanism of spontaneous formation of ribonucleotides under realistic prebiotic conditions is a key open issue of origins-of-life research. In cells, de novo and salvage nucleotide enzymatic synthesis combines 5-phospho-α-d-ribose-1-diphosphate (α-PRPP) and nucleobases. Interestingly, these reactants are also known as prebiotically plausible compounds.

Hydrothermal Decomposition of Amino Acids and Origins of Prebiotic Meteoritic Organic Compounds.

The organic compounds found in carbonaceous chondrite meteorites provide insight into primordial solar system chemistry. Evaluating the formation and decomposition mechanisms of meteoritic amino acids may aid our understanding of the origins of life and homochirality on Earth. The amino acid glycine is widespread in meteorites and other extraterrestrial environments; other amino acids, such as isovaline, are found with enantiomeric excesses in some meteorites.

Accurate multiple time step in biased molecular simulations.

Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a bottleneck in molecular dynamics simulations. An algorithm to treat smooth biasing forces within a multiple time step framework is here discussed.

ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations.

Non-structural protein 3 (NS3) helicase from hepatitis C virus is an enzyme that unwinds and translocates along nucleic acids with an ATP-dependent mechanism and has a key role in the replication of the viral RNA. An inchworm-like mechanism for translocation has been proposed based on crystal structures and single molecule experiments. We here perform atomistic molecular dynamics in explicit solvent on the microsecond time scale of the available experimental structures.