Molecular reaction dynamics is the study of chemical and physical transformations of matter at the molecular level. The understanding of how chemical reactions occur and how to control them is ...fundamental to chemists and interdisciplinary areas such as materials and nanoscience, rational drug design, environmental and astrochemistry. This book provides a thorough foundation to this area. The first half is introductory, detailing experimental techniques for initiating and probing reaction dynamics and the essential insights that have been gained. The second part explores key areas including photoselective chemistry, stereochemistry, chemical reactions in real time and chemical reaction dynamics in solutions and interfaces. Typical of the new challenges are molecular machines, enzyme action and molecular control. With problem sets included, this book is suitable for advanced undergraduate and graduate students, as well as being supplementary to chemical kinetics, physical chemistry, biophysics and materials science courses, and as a primer for practising scientists.
An Electronic Time Scale in Chemistry Remacle, F.; Levine, R. D.
Proceedings of the National Academy of Sciences,
05/2006, Letnik:
103, Številka:
18
Journal Article, Web Resource
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Ultrafast, subfemtosecond charge migration in small peptides is discussed on the basis of computational studies and compared with the selective bond dissociation after ionization as observed by ...Schlag and Weinkauf. The reported relaxation could be probed in real time if the removal of an electron could be achieved on the attosecond time scale. Then the mean field seen by an electron would be changing rapidly enough to initiate the migration. Tyrosine-terminated tetrapeptides have a particularly fast charge migration where in <1 fs the charge arrives at the other end. A femtosecond pulse can be used to observe the somewhat slower relaxation induced by correlation between electrons of different spins. A slower relaxation also is indicated when removing a deeper-lying valence electron. When a chromophoric amino acid is at one end of the peptide, the charge can migrate all along the peptide backbone up to the N end, but site-selective ionization is probably easier to detect for tryptophan than for tyrosine.
Intercommunication between dynamic chemical networks plays a major role in cellular transformations. Inspired by nature, we introduce the intercommunication between two constitutional dynamic ...networks, CDNs, “S” and “T” composed, each, of four equilibrated supramolecular constituents AA′, AB′, BA′, and BB′, and of CC′, CD′, DC′, and DD′, respectively. Each of the constituents is conjugated to a Mg2+-ion-dependent DNAzyme unit that acts as a reporter element for the concentration of the respective constituent via the catalyzed cleavage of the fluorophore/quencher-functionalized substrate associated with the respective DNAzyme reporter. Also, constituents BB′ (in CDN “S”) and CC′ (in CDN “T”) include Mg2+-ion-dependent DNAzymes acting as activator units for generating triggering signals between the networks. Subjecting CDNs “S” and “T” to the catalytically cleavable hairpin trigger Hdd′ or Haa′, respectively, yields input strands that intercommunicate the CDNs by affecting the time-dependent re-equilibration of the constituents of the counter CDN without affecting the dynamic equilibrium of the constituents of the CDN that generates the triggering strands. Treatment of CDNs “S” and “T” with hairpins Hdd′ and Haa′ (or Hba′), respectively, stimulates autonomous positive/positive or positive/negative feedback to the programmed time-dependent up-regulation or down-regulation of the equilibrated constituents in the two CDNs.
Our information theoretic considerations suggest that the essence of phase transitions in condensed matter is the change in entropy as reflected in the change in the number of isomers between two ...phases. The explicit number of isomers as a function of size is computed using a graph theoretic approach that is compared to a direct count for smaller systems. This allows us to apply a common approach to both nanosystems and their macroscopic limit. The entropy increases very rapidly with size with the results that replacing the actual distribution over size by an average is not an accurate approximation. That the phase transition is a sharp function of the temperature is due to the high heat capacity of both the solid and liquid phases. The difference in entropy at the transition is related to the Trouton-Richards considerations. The finite width of the boundary between two phases of a finite system is related to the inherent uncertainty product that is derived from the maximum entropy formalism and that is a result of the fluctuations about equilibrium. As the system size increases, the boundary becomes sharper and one recovers the usual thermodynamic description.
Protein abundance and phosphorylation convey important information about pathway activity and molecular pathophysiology in diseases including cancer, providing biological insight, informing drug and ...diagnostic development, and guiding therapeutic intervention. Analyzed tissues are usually collected without tight regulation or documentation of ischemic time. To evaluate the impact of ischemia, we collected human ovarian tumor and breast cancer xenograft tissue without vascular interruption and performed quantitative proteomics and phosphoproteomics after defined ischemic intervals. Although the global expressed proteome and most of the >25,000 quantified phosphosites were unchanged after 60 min, rapid phosphorylation changes were observed in up to 24% of the phosphoproteome, representing activation of critical cancer pathways related to stress response, transcriptional regulation, and cell death. Both pan-tumor and tissue-specific changes were observed. The demonstrated impact of pre-analytical tissue ischemia on tumor biology mandates caution in interpreting stress-pathway activation in such samples and motivates reexamination of collection protocols for phosphoprotein analysis.
A quantum machine that accepts an input and processes it in parallel is described. The logic variables of the machine are not wavefunctions (qubits) but observables (i.e., operators) and its ...operation is described in the Heisenberg picture. The active core is a solid-state assembly of small nanosized colloidal quantum dots (QDs) or dimers of dots. The size dispersion of the QDs that causes fluctuations in their discrete electronic energies is a limiting factor. The input to the machine is provided by a train of very brief laser pulses, at least four in number. The coherent band width of each ultrashort pulse needs to span at least several and preferably all the single electron excited states of the dots. The spectrum of the QD assembly is measured as a function of the time delays between the input laser pulses. The dependence of the spectrum on the time delays can be Fourier transformed to a frequency spectrum. This spectrum of a finite range in time is made up of discrete pixels. These are the visible, raw, basic logic variables. The spectrum is analyzed to determine a possibly smaller number of principal components. A Lie-algebraic point of view is used to explore the use of the machine to emulate the dynamics of other quantum systems. An explicit example demonstrates the considerable quantum advantage of our scheme.
The Pneumonia Etiology Research for Child Health (PERCH) project is a 7-country, standardized, comprehensive evaluation of the etiologic agents causing severe pneumonia in children from developing ...countries. During previous etiology studies, between one-quarter and one-third of patients failed to yield an obvious etiology; PERCH will employ and evaluate previously unavailable innovative, more sensitive diagnostic techniques. Innovative and rigorous epidemiologic and analytic methods will be used to establish the causal association between presence of potential pathogens and pneumonia. By strategic selection of study sites that are broadly representative of regions with the greatest burden of childhood pneumonia, PERCH aims to provide data that reflect the epidemiologic situation in developing countries in 2015, using pneumococcal and Haemophilus influenzae type b vaccines. PERCH will also address differences in host, environmental, and/or geographic factors that might determine pneumonia etiology and, by preserving specimens, will generate a resource for future research and pathogen discovery.
A nucleic acid-based constitutional dynamic network (CDN) is introduced as a single computational module that, in the presence of different sets of inputs, operates a variety of logic gates including ...a half adder, 2 : 1 multiplexer and 1 : 2 demultiplexer, a ternary multiplication matrix and a cascaded logic circuit. The CDN-based computational module leads to four logically equivalent outputs for each of the logic operations. Beyond the significance of the four logically equivalent outputs in establishing reliable and robust readout signals of the computational module, each of the outputs may be fanned out, in the presence of different inputs, to a set of different logic circuits. In addition, the ability to intercommunicate constitutional dynamic networks (CDNs) and to construct DNA-based CDNs of higher complexity provides versatile means to design computing circuits of enhanced complexity.
A nucleic acid-based constitutional dynamic network (CDN) provides a single functional computational module for diverse input-guided logic operations and computing circuits.
Toward identifying a cancer-specific gene signature we applied surprisal analysis to the RNAs expression behavior for a large cohort of breast, lung, ovarian, and prostate carcinoma patients. We ...characterize the cancer phenotypic state as a shared response of a set of mRNA or microRNAs (miRNAs) in cancer patients versus noncancer controls. The resulting signature is robust with respect to individual patient variability and distinguishes with high fidelity between cancer and noncancer patients. The mRNAs and miRNAs that are implicated in the signature are correlated and are known to contribute to the regulation of cancer-signaling pathways. The miRNA and mRNA networks are common to the noncancer and cancer patients, but the disease modulates the strength of the connectivities. Furthermore, we experimentally assessed the cancer-specific signatures as possible therapeutic targets. Specifically we restructured a single dominant connectivity in the cancer-specific gene network in vitro. We find a deflection from the cancer phenotype, significantly reducing cancer cell proliferation and altering cancer cellular physiology. Our approach is grounded in thermodynamics augmented by information theory. The thermodynamic reasoning is demonstrated to ensure that the derived signature is bias-free and shows that the most significant redistribution of free energy occurs in programming a system between the noncancer and cancer states. This paper introduces a platform that can elucidate miRNA and mRNA behavior on a systems level and provides a comprehensive systematic view of both the energetics of the expression levels of RNAs and of their changes during tumorigenicity.
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