physics.bio-ph Archives

Topological alteration of a state graph. a) A system being coarse-grained and receiving arbitrary labels from an external observer. The example macrostate (u) labels are vectors of three binary-valued microstate variables denoted (v1, v2, v3). Panels b to d display the topologies of the physicallyreachable state graph after constraining a variable of the labeling vector. The nodes and edges that became inaccessible as a consequence of applying a conservation law are displayed with lighter colors. The top row corresponds to setting value 0, while the bottom row corresponds to setting the variable to 1. b) Constraining variable v1. On the one hand (b.1), a conservation law for v1 = 0 leads the system to state u1. On the other hand (b.2), with v1 = 1, the system cannot escape from u2. c) Constraining variable v1. In the case v1 = 1 in c.2), the graph is restricted to u3 and has no possible transitions. The node does exist under a conservation law setting v1 to 1 but there is no way to reach this node due to the topology of the unconstrained graph. d) Constraining variable v3. This variable is constant and equal to 1 in the unconstrained graph in a), so a conservation law setting v3 = 0 such as in panel d.1 is meaningless for this case. -- physics.bio-ph

Biophysics, Biosignatures & Paleobiology, Nanotechnology & SynBio, Origin & Evolution of Life, Status Report

An Open-Ended Approach to Understanding Local, Emergent Conservation Laws in Biological Evolution

by Keith CowingSeptember 24, 2024September 24, 2024

While fields like Artificial Life have made huge strides in quantifying the mechanisms that distinguish living systems from non-living ones, particular mechanisms remain difficult to reproduce in silico.

Polymetallic nodules on the seafloor -- NOAA

Atmospheres, Climate, Weather, Biogeochemical Cycles & Geobiology, Biophysics, Biosignatures & Paleobiology, Enceladus, Europa, Extremeophiles and Extreme Environments, Habitable Zones, Icy Worlds, Microbiology & Virology, ROVs/Submersibles/Diving, Status Report, Water/Hycean Worlds & Oceanography

Dwellers In The Deep: Biological Consequences Of Dark Oxygen

by Keith CowingAugust 15, 2024August 15, 2024

The striking recent putative detection of “dark oxygen” (dark O2) sources on the abyssal ocean floor in the Pacific at ∼4 km depth raises the intriguing scenario that complex (i.e., […]

(a) Formation process of the ribose from 10 (Z)-ethene-1,2-diol, 5 formaldehyde, and 5 water under the condition of 10 GPa - 1400 K. (b) Free energy landscape for analyzing the formation process of ribose, as a function of two kinds of C-C distance as the collective variables. To better distinguish the selected carbon atoms, C1 and C2 are marked by yellow and orange colors, respectively. (c) The evolution process of the ribose from the open chain to a five-membered ring (10 GPa - 1400 K). (d) Comparison of the formation ability of five-membered ring and sixmembered ring based on the free energy calculation with the C-O distance as the collective variable. -- physics.bio-ph

Astrogeology, Atmospheres, Climate, Weather, Biochemistry & Organic Chemistry, Biogeochemical Cycles & Geobiology, Biosignatures & Paleobiology, Extremeophiles and Extreme Environments, Fossils & Paleontology, Habitable Zones, Status Report, Water/Hycean Worlds & Oceanography

Synthesis And Stability Of Biomolecules Under Earth’s Upper Mantle Conditions

by Keith CowingMay 9, 2024

How life started on Earth is a long-time unsolved mystery. There are various hypotheses ranging from outer space to seabed.

Mass spectrum of the soluble extract from room temperature residual (C, CO, NH3, and H2O reactants). The molecular structures assigned to the peaks are shown without Na+, which is added during the ionization. -- physics.bio-ph

Astrochemistry, Astronomy & Telescopes, Biochemistry & Organic Chemistry, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Imaging & Spectroscopy, Interstellar, Origin & Evolution of Life, Status Report

Formation Of Extraterrestrial Peptides And Their Derivative

by Keith CowingMay 3, 2024May 3, 2024

The formation of protein precursors, due to the condensation of atomic carbon under the low-temperature conditions of the molecular phases of the interstellar medium, opens alternative pathways for the origin […]

Guanosine-5'-triphosphate (GTP) -- Wikipedia

Biochemistry & Organic Chemistry, Biophysics, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

GTP Before ATP: The Energy Currency At The Origin Of Genes

by Keith CowingMarch 24, 2024March 24, 2024

Life is an exergonic chemical reaction. Many individual reactions in metabolism entail slightly endergonic processes that are coupled to free energy release, typically as ATP hydrolysis, in order to go […]

Random interactions reproduce the aggregate diversity observed in simple interaction maps. For each value of affinity and asymmetry, we show a randomly drawn interaction map (bottom left matrix, with the color scale of Fig. 3), a snapshot of the result of the simulated annealing, and the aggregate category, as in Fig. 2. Here and in the following, the lattice has 30 × 30 sites, and there are 100 particles. -- physics.bio-ph

Biochemistry & Organic Chemistry, Biophysics, Nanotechnology & SynBio, Origin & Evolution of Life, Status Report

How Do Particles With Complex Interactions Self-assemble?

by Keith CowingDecember 28, 2023

In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches.

The mechanism of spin-selective crystallization due to the CISS effect and the experimental setup. a. As molecules approach a surface, they transiently acquire an induced charge polarization. Due to the CISS effect, transient charge polarization of a chiral molecule is accompanied by spin polarization. The spin state associated with the charge poles is determined by the handedness of the chiral molecule. Because the magnetic surface itself is spin polarized it kinetically favors (akin to a seed crystal) the enantiomer whose transient spin state results in a lower energy spin-exchange interaction. The lower energy overlap with the magnetic surface is singlet-like (red, ↑↓) and the higher energy overlap is triplet-like (blue, ↑↑). The energy difference between these two configurations is higher than the room temperature, kBT, therefore the effect robustly manifests itself. b. Schematic of the setup used in the crystallization experiments and a sample microscope image of the RAO crystals on a magnetite surface from a direct crystallization experiment. The image shows the magnetite surface as the black background and the needle-shaped conglomerate crystals of RAO formed on the surface, as well as the twinned crystals with stochastically arranged needles of D and L-RAO, and racemic RAO in the form of a flaky powder suspended in the water column above the surface. -- physics.chem-ph

Biochemistry & Organic Chemistry, Biophysics, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

Origin of Biological Homochirality by Crystallization of an RNA Precursor on a Magnetic Surface

by Keith CowingJune 16, 2023June 16, 2023

Homochirality is a signature of life on Earth yet its origins remain an unsolved puzzle. Achieving homochirality is essential for a high-yielding prebiotic network capable of producing functional polymers like […]

Inferring Molecular Assembly from infrared spectroscopy. (A) XTB-calculated IR spectrum of 5-aminoisophthalic acid with highlighted fingerprint region (400–1500 cm–1 ). (B) Example of the six most intense vibrational bands in the fingerprint region demonstrating its collective-motion nature. (C) Assembly index vs. IR-inferred assembly index estimated from the number of IR peaks in the fingerprint region (400–1500 cm–1 ) based on XTB calculation on 10,000 molecules (see Eq. 1). Correlation between the predicted and expected assembly index is 0.86. (D) Assembly index vs. IR-inferred assembly index estimated from the number of IR peaks in the fingerprint region (400–1500 cm–1 ) based on the experimental measurement on 99 molecules (see Eq. 2). Correlation between the predicted and expected assembly index is 0.75. -- physics.bio-ph

Astrochemistry, Astronomy & Telescopes, Biosignatures & Paleobiology, Imaging & Spectroscopy, Status Report

Multimodal Techniques For Detecting Alien Life Using Assembly Theory And Spectroscopy

by Keith CowingMarch 20, 2023March 20, 2023

Detecting alien life is a difficult task because it’s hard to find signs of life that could apply to any life form. However, complex molecules could be a promising indicator […]

Astrogeology, Biosignatures & Paleobiology, Cryobiology, Extremeophiles and Extreme Environments, Icy Worlds, Microbiology & Virology, Press Release

Biolocomotion And Premelting In Ice

by Keith CowingJuly 10, 2022February 4, 2023

Biota are found in glaciers, ice sheets and permafrost. Ice bound micro-organisms evolve in a complex mobile environment facilitated or hindered by a range of bulk and surface interactions.

Astrochemistry

Polarized Muons And The Origin Of Biological Homochirality

by Keith CowingOctober 5, 2021

While biologists have not yet reached a consensus on the definition of life, homochirality – the specific molecular handedness of biomolecules – is a phenomenon only produced by life. The […]