Control of time-dependent biological processes by temporally patterned input

Temporal patterning of biological variables, in the form of oscillations and rhythms on many time scales, is ubiquitous. Altering the temporal pattern of an input variable greatly affects the output of many biological processes. We develop here a conceptual framework for a quantitative understanding of such pattern dependence, focusing particularly on nonlinear, saturable, time-dependent processes that abound in biophysics, biochemistry, and physiology. We show theoretically that pattern dependence is governed by the nonlinearity of the input–output transformation as well as its time constant. As a result, only patterns on certain time scales permit the expression of pattern dependence, and processes with different time constants can respond preferentially to different patterns. This has implications for temporal coding and decoding, and allows differential control of processes through pattern. We show how pattern dependence can be quantitatively predicted using only information from steady, unpatterned input. To apply our ideas, we analyze, in an experimental example, how muscle contraction depends on the pattern of motorneuron firing.

Vibrational population relaxation of carbon monoxide in the heme pocket of photolyzed carbonmonoxy myoglobin: Comparison of time-resolved mid-IR absorbance experiments and molecular dynamics simulations

The vibrational energy relaxation of carbon monoxide in the heme pocket of sperm whale myoglobin was studied by using molecular dynamics simulation and normal mode analysis methods. Molecular dynamics trajectories of solvated myoglobin were run at 300 K for both the δ- and ɛ-tautomers of the distal His-64. Vibrational population relaxation times of 335 ± 115 ps for the δ-tautomer and 640 ± 185 ps for the ɛ-tautomer were estimated by using the Landau–Teller model. Normal mode analysis was used to identify those protein residues that act as the primary “doorway” modes in the vibrational relaxation of the oscillator. Although the CO relaxation rates in both the ɛ- and δ-tautomers are similar in magnitude, the simulations predict that the vibrational relaxation of the CO is faster in the δ-tautomer with the distal His playing an important role in the energy relaxation mechanism. Time-resolved mid-IR absorbance measurements were performed on photolyzed carbonmonoxy hemoglobin (Hb13CO). From these measurements, a T1 time of 600 ± 150 ps was determined. The simulation and experimental estimates are compared and discussed.

An endogenous rate of time preference, the Penrose effect, and dynamic optimality of environmental quality.

In the present paper, the endogenous theory of time preference is extended to analyze those processes of capital accumulation and changes in environmental quality that are dynamically optimum with respect to the intertemporal preference ordering of the representative individual of the society in question. The analysis is carried out within the conceptual framework of the dynamic analysis of environmental quality, as has been developed by a number of economists for specific cases of the fisheries and forestry commons. The duality principles on intertemporal preference ordering and capital accumulation are extended to the situation where processes of capital accumulation are subject to the Penrose effect, which exhibit the marginal decrease in the effect of investment in private and social overhead capital upon the rate at which capital is accumulated. The dynamically optimum time-path of economic activities is characterized by the proportionality of two systems of imputed, or efficient, prices, one associated with the given intertemporal ordering and another associated with processes of accumulation of private and social overhead capital. It is particularly shown that the dynamically optimality of the processes of capital accumulation involving both private and social overhead capital is characterized by the conditions that are identical with those involving private capital, with the role of social overhead capital only indirectly exhibited.