A natural feature of molecular systems is their inherent stochastic behavior. A fundamental challenge related to the programming of molecular information processing systems is to develop a circuit architecture that controls the stochastic states of individual molecular events. Here we present a systematic implementation of probabilistic switching circuits, using DNA strand displacement reaction...

floorplanning is an important step in physical design of vlsi circuits. it is used to plan the positions of a set of circuit modules on a chip in order to optimize the circuit performance. however, modern floorplanning takes better care of providing extra options to place dedicated modules in the hierarchical designs to align circuit blocks one by one within certain bounding box for helping seq...

Computation using biological Deoxyribonucleic acid (DNA) strand is increasingly found to be a viable proposition. A unique generalized efficient algorithm for forming any Boolean circuit strand is proposed in this paper. The implementation of the Boolean circuit using the proposed algorithm is also presented. This Boolean circuit requires only one kind of bio-operation at each level. Further, t...

This paper examines several polynomials related to the field of graph theory including the circuit partition polynomial, Tutte polynomial, and the interlace polynomial. We begin by explaining terminology and concepts that will be needed to understand the major results of the paper. Next, we focus on the circuit partition polynomial and its equivalent, the Martin polynomial. We examine the resul...

The bacterial SOS stress-response pathway is a pro-mutagenic DNA repair system that mediates bacterial survival and adaptation to genotoxic stressors, including antibiotics and UV light. The SOS pathway is composed of a network of genes under the control of the transcriptional repressor, LexA. Activation of the pathway involves linked but distinct events: an initial DNA damage event leads to ac...

DNA methyltransferase 1 (DNMT1) is responsible for copying DNA methylation patterns to the daughter strands during DNA replication. Its expression is frequently up-regulated in human tumors, including hepatocellular carcinoma, but the mechanism of overexpression and its biological significance remain unclear. Here, we show that hepatitis B virus X protein (HBx) activates DNMT1 expression via a ...

CAD plays a fundamental role in both top-down and bottom-up system fabrication. This paper presents a bottom-up circuit patterning process based on DNA selfassembly in terms of the design tool requirements and the new opportunities self-assembly creates for circuit designers. The paper also connects recent demonstrations of addressable selfassembly to applications in computer architecture and s...