Memory effects and static disorder reduce information in single-molecule signals

A key theoretical challenge posed by single-molecule studies is the inverse problem of deducing the underlying molecular dynamics from the time evolution of low-dimensional experimental observables. Toward this goal, a variety of low-dimensional models have been proposed as descriptions of single-molecule signals, including random walks with or without conformational memory and/or with static or dynamics disorder. Differentiating among different models presents a challenge, as many distinct physical scenarios lead to similar experimentally observable behaviors such as anomalous diffusion and nonexponential relaxation. Here we show that information-theory-based analysis of single-molecule time series, inspired by Shannon's work studying the information content of printed English, can differentiate between Markov (memoryless) and non-Markov single-molecule signals and between static and dynamic disorder. In particular, non-Markov time series are more predictable and thus can be compressed and transmitted within shorter messages (i.e. have a lower entropy rate) than appropriately constructed Markov approximations, and we demonstrate that in practice the LZMA compression algorithm reliably differentiates between these entropy rates across several simulated dynamical models.

Formic Acid Ionization and Fragmentation by Multiphoton Absorption

Multiphoton absorption is an intensity dependent nonlinear effect related to the excitation of virtual intermediate states. In the present work, multiphoton ionization and dissociation of the formic acid molecule (HCOOH) by the interaction with photons from 532 Nd: YAG laser at different intensities are discussed, using different carrier gases. The induced fragmentation-ionization patterns show up to 17 fragments and dissociation channels are proposed. Some evidence of small clusters formation and conformational memory from the ratio of the detected products, CO+ and CO2+, on the light of the available results, it is possible to conclude that they arise from trans and cis formic acid. Our results are compared with those obtained in other laboratories under different experimental conditions, some of them show only partial agreement and differences are discussed. Following the Keldysh description it is possible, from our experimental parameters, characterize our results, in the multiphoton absorption regime.

Imparting Conformational Memory for Material Adhesion

Adhesion between similar and dissimilar materials is essential to many biological systems and synthetic materials, devices, and machines. Since the inception of adhesion science more than five decades ago, adhesion...

Viral Genome Conformations and Contacts across Different Lifecycle Stages

Single-stranded RNA viral genomes (gRNA) are dynamic molecules that permit packaging into virions and their subsequent extrusion during infection. For viruses with such genomes, we discovered a previously unsuspected mechanism that regulates their assembly. This regulation is the result of multiple cognate coat protein (CP)–gRNA contacts distributed across the RNA. Collectively, these interactions make the assembly highly efficient and specific. The regions of the gRNA packaging signals (PSs) driving this assembly are potential drug targets, whilst the manipulation of PS–CP contacts with nonviral RNA cargos is a route towards bespoke virus-like particles. Infectivity depends on the virions being able to transfer their gRNAs into host cells. The starting point for this transfer appears to be an encapsidated RNA with a defined three-dimensional structure, especially around the PSs. A combination of asymmetric cryo-electron microscopy structure determination and X-ray synchrotron footprinting were used to define these contacts and structures in a number of viral examples, including hepatitis B virus and enteroviruses. These tools allow us to look beyond the outer CP layer of the virion shell and to see the functional, asymmetric components that regulate viral infectivity. This revealed yet more unexpected aspects of critical infection mechanisms, such as the RNA conformational changes required for encapsidation, the details of PS–CP contacts regulating the assembly, and the conformational “memory” imposed by encapsidation.

Molecular electronics based on self-assembled monolayers

This article considers molecular electronics based on self-assembled monolayers. It begins with a brief overview of the nanofabrication of molecular devices, followed by a discussion of the electronic properties of several basic devices, from simple molecules such as molecular tunnel junctions and molecular semiconducting wires, to more complex ones such as molecular rectifying diodes. It also describes molecular switches and memories, focusing on three approaches called ‘conformational memory’, ‘charge-based memory’ and ‘RTD-based memory’ (RTD is resonant tunnelling diode). It shows that memory can be implemented from resonant tunnelling diodes following cell architecture already used for semiconductor devices. The article concludes with a review of molecular transistors.

Chemo-ionic-conformational memory from reactive dense gels: a way to explore new multivalent memories and brain memory

ABSTRACTSo far we ignore how brain stores memory. Neurons communicate by pulses where the charges are carried between them by ions flowing through channels. Those pulses present a characteristic maximum related to the conformational movements of the channel protein opening and closing. Electrochemical responses from dense gel electrodes of conducting polymers mimic those pulses. Here we proved that the biomimetic pulse includes simultaneously electrical, chemical and conformational information related to the energy stored by the initial conformational packed state of the polymer. This energetic memory increases linearly with the potential used to reduce and pack (write) the initial state: hundreds of different values can be written (stored) in a full reproducible way (multivalent memory). Every state constitutes a chemo-ionic-conformational (CHEMICONF) memory. Each multivalent memory is read and erased by the reverse electrochemical reaction. Crosslinking states produce permanent memories not erased while reading. Developing CHEMICONF memories can provide new hypothesis to reveal brain memory mechanisms.