Research - Revision history

MarcRiedel: Correct typos, grammar, formatting, and bibliographic errors

2026-08-30T01:12:41Z

Correct typos, grammar, formatting, and bibliographic errors

MarcRiedel: Replace obsolete Publications redirects with the canonical page link

2026-08-10T15:04:25Z

Replace obsolete Publications redirects with the canonical page link

← Older revision		Revision as of 15:04, 10 August 2026
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	[[Image:moving-average-filter-simulation.gif\|center\|thumb\|400px\|Simulations of DNA implementation of a '''moving-average FIR filter'''. This filter removes the high-frequency component from an input signal, producing an output signal consisting of only the low-frequency component. Here the "signals" are molecular concentrations.]]		[[Image:moving-average-filter-simulation.gif\|center\|thumb\|400px\|Simulations of DNA implementation of a '''moving-average FIR filter'''. This filter removes the high-frequency component from an input signal, producing an output signal consisting of only the low-frequency component. Here the "signals" are molecular concentrations.]]

	Please see our "[[Papers,_Theses,~~_and_Presentations~~ \|Publications]]" page for more of our papers on these topics.		Please see our "[[Papers,_Presentations,_Theses,_and_Patents \|Publications]]" page for more of our papers on these topics.

	==Computational Immunology==		==Computational Immunology==
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	<br>		<br>
	[//mriedel.ece.umn.edu/wiki/images/b/b0/Najafi_Jamali_Zavareh_Lilja_Riedel_Bazargan_Harjani_Time_Encoded_Values_for_Highly_Efficient_Stochastic_Circuits.pdf Paper]		[//mriedel.ece.umn.edu/wiki/images/b/b0/Najafi_Jamali_Zavareh_Lilja_Riedel_Bazargan_Harjani_Time_Encoded_Values_for_Highly_Efficient_Stochastic_Circuits.pdf Paper]
	\|}Please see our "[[Papers,_Theses,~~_and_Presentations~~ \|Publications]]" page for more of our papers on these topics.		\|}Please see our "[[Papers,_Presentations,_Theses,_and_Patents \|Publications]]" page for more of our papers on these topics.

	==Computing with Feedback==		==Computing with Feedback==
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	<br> [http://mriedel.ece.umn.edu/files/Riedel_Cyclic_Combinational_Circuits.ppt Slides]		<br> [http://mriedel.ece.umn.edu/files/Riedel_Cyclic_Combinational_Circuits.ppt Slides]
	\|}		\|}
	Please see our [[Papers,_Theses,~~_and_Presentations~~ \| Publications]] page for more of our papers on this topic.		Please see our [[Papers,_Presentations,_Theses,_and_Patents \| Publications]] page for more of our papers on this topic.


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	<br> [http://mriedel.ece.umn.edu/wiki/images/f/fe/Altun_Riedel_Neuhauser_Nanoscale_Digital_Computation_Through_Percolation.ppt Slides]		<br> [http://mriedel.ece.umn.edu/wiki/images/f/fe/Altun_Riedel_Neuhauser_Nanoscale_Digital_Computation_Through_Percolation.ppt Slides]
	\|}		\|}
	Please see our "[[Papers,_Theses,~~_and_Presentations~~ \|Publications]]" page for more of our papers on these topics.		Please see our "[[Papers,_Presentations,_Theses,_and_Patents \|Publications]]" page for more of our papers on these topics.

	==Algorithms and Data Structures==		==Algorithms and Data Structures==
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	<br> [http://mriedel.ece.umn.edu/wiki/images/0/00/Backes_Riedel_Reduction_Of_Interpolants_For_Logic_Synthesis.ppt Slides]		<br> [http://mriedel.ece.umn.edu/wiki/images/0/00/Backes_Riedel_Reduction_Of_Interpolants_For_Logic_Synthesis.ppt Slides]
	\|}		\|}
	Please see our "[[Papers,_Theses,~~_and_Presentations~~ \|Publications]]" page for more of our papers on this topic. (Papers on SAT-based circuit verification, that is, not on squids.)		Please see our "[[Papers,_Presentations,_Theses,_and_Patents \|Publications]]" page for more of our papers on this topic. (Papers on SAT-based circuit verification, that is, not on squids.)

	==Mathematics==		==Mathematics==
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	\|}		\|}

	Please see our "[[Papers,_Theses,~~_and_Presentations~~ \|Publications]]" page for more of our papers on this topic.		Please see our "[[Papers,_Presentations,_Theses,_and_Patents \|Publications]]" page for more of our papers on this topic.

MarcRiedel: /* Computing with Random Bit Streams */

2026-05-05T18:03:39Z

Computing with Random Bit Streams

← Older revision		Revision as of 18:03, 5 May 2026
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	{\| align="center"		{\| align="center"
	\| [[Image:stochastic-multiplier.png\|center\|thumb\|350px\|'''Multiplication''' with an AND gate. Here the variables represents the ''probabilities'' of obtaining a 1 versus a 0 in stochastic bit streams. The AND gate produces an output probability ~~<math>~~c~~</math>~~ that is the product of the of the input probabilities ~~<math>~~a~~</math>~~ and ~~<math>~~b~~</math>~~.]]		\| [[Image:stochastic-multiplier.png\|center\|thumb\|350px\|'''Multiplication''' with an AND gate. Here the variables represents the ''probabilities'' of obtaining a 1 versus a 0 in stochastic bit streams. The AND gate produces an output probability c that is the product of the of the input probabilities a and b.]]
	\|\|		\|\|
	\|\| [[Image:stochastic-adder.png\|thumb\|320px\|'''Scaled addition''' with a multiplexer (MUX).		\|\| [[Image:stochastic-adder.png\|thumb\|320px\|'''Scaled addition''' with a multiplexer (MUX).
	Given input probabilities <math>a</math>, ~~<math>~~b~~</math>~~ and ~~<math>~~s~~</math>~~, the MUX produces an output probability ~~<math>~~c = a s + (1 - s) b~~</math>~~.]]		Given input probabilities <math>a</math>, b and s, the MUX produces an output probability c = a s + (1 - s) b.]]
	\|}		\|}

MarcRiedel: /* Computational Immunology */

2025-07-24T21:31:05Z

Computational Immunology

← Older revision		Revision as of 21:31, 24 July 2025
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	\|}		\|}

	The binding is a critical step in a critical component of the immune system: it allows circulating '''T-cells to kill off infected cells.''' If this mechanism succeeds, an infection is stopped in its tracks. If it fails, then infected cells become factories for reproducing copies of the virus; full-blown disease results. Given a novel pathogen, such as SARS-Cov-2, predicting whether the immune system of an individual will do its job at fighting off the disease comes down to predicting how well the viral peptides bind to the cell-surface receptors of that person. We are tackling the problem with cloud computing resources, donated by [https://blogs.oracle.com/research/post/announcing-inaugural-cohort-oracle-research-fellows Oracle]:		The binding is a critical step in a critical component of the immune system: it allows circulating '''T-cells to kill off infected cells.''' If this mechanism succeeds, an infection is stopped in its tracks. If it fails, then infected cells become factories for reproducing copies of the virus; full-blown disease results. Given a novel pathogen, such as SARS-Cov-2, predicting whether the immune system of an individual will do its job at fighting off the disease comes down to predicting how well the viral peptides bind to the cell-surface receptors of that person. We are tackling the problem with cloud computing resources, donated by [https://blogs.oracle.com/research/post/announcing-inaugural-cohort-oracle-research-fellows Oracle].
	{\|		{\|
	\|		\|
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	\|- valign="top"		\|- valign="top"
	\| width="100" \| '''title''':		\| width="100" \| '''title''':
			\| width="500" \| [https://mriedel.ece.umn.edu/wiki/images/2/2d/Atkins_Solanki_Vasmatzis_Cornette_Riedel_Geographically_Biased_Composition_of_NetMHCpan_Training_Datasets_and_Evaluation_of_MHC-Peptide_Binding_Prediction_Accuracy_on_Novel_Alleles.pdf Geographically Biased Composition of NetMHCpan Training Datasets and Evaluation of MHC-Peptide]
	\| width="500" \| [https://mriedel.ece.umn.edu/wiki/images/d/d5/UMN_Mayo_CHIP_Center.pdf The UMN/Mayo Computational Human Immuno-Peptidome (CHIP) Project]
⚫	\|- valign="top"
	\| '''Investigator''':
	\| [[Marc Riedel]]
	\|- valign="top"		\|- valign="top"
	\| '''~~Agency~~''':		\| '''authors''':
			\| Thomas Atkins, [[Arnav Solanki]], [https://www.mayo.edu/research/faculty/vasmatzis-george-ph-d/bio-00027811 George Vasmatzis], [https://orion.math.iastate.edu/cornette/ James Cornette], and [[Marc Riedel]]
	\| [https://www.oracle.com/research/ Oracle]
	\|- valign="top"		\|- valign="top"
	\| '''~~Program~~''':		\| '''appeared in''':
			\| [https://www.frontiersin.org/journals/immunology Frontiers in Immunology], Vol. 14, 2023
	\| [https://blogs.oracle.com/research/post/announcing-inaugural-cohort-oracle-research-fellows Oracle Research Fellowship]
			\|}
			\| align="center" width="70" \|
			<span class="plainlinks">
			[https://www.frontiersin.org/articles/10.3389/fimmu.2023.1288105/full http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
			<br>
			[https://www.frontiersin.org/articles/10.3389/fimmu.2023.1288105/full Paper]
			\|}

			{\|
			\|
			{\| style="background:#F0E68C"
		⚫	\|- valign="top"
			\| width="100" \| '''title''':
			\| width="500" \| [[Media:Evasive_Spike_Variants_Elucidate_the_Preservation_of_T_Cell_Immune_Response_to_the_SARS-CoV-2_Omicron_Variant.pdf\|Evasive Spike Variants Elucidate the Preservation of T cell Immune Response to the SARS-CoV-2 Omicron Variant]]
	\|- valign="top"		\|- valign="top"
	\| '''~~Award~~''':		\| '''authors''':
			\| [[Arnav Solanki]], [[Marc Riedel]], [https://orion.math.iastate.edu/cornette/ James Cornette], [[Julia Udell]], and [https://www.mayo.edu/research/faculty/vasmatzis-george-ph-d/bio-00027811 George Vasmatzis]
	\| $200,000
	\|- valign="top"		\|- valign="top"
	\| '''~~Duration~~''':		\| '''appeared in''':
			\| [https://ieeexplore.ieee.org/document/10457533 IEEE/ACM Trans. on Computational Biology and Bioinformatics], pp. 1–11, March, 2024
	\| 2022 – 2024
	\|}		\|}
	\| width="70" align="center" \|		\| width="70" align="center" \|
	<span class="plainlinks">		<span class="plainlinks">
	[https://mriedel.ece.umn.edu/wiki/images/d/d5/~~UMN_Mayo_CHIP_Center~~.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>		[https://mriedel.ece.umn.edu/wiki/images/1/12/Evasive_Spike_Variants_Elucidate_the_Preservation_of_T_Cell_Immune_Response_to_the_SARS-CoV-2_Omicron_Variant.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>
			<br>
	<br>[https://mriedel.ece.umn.edu/wiki/images/d/d5/UMN_Mayo_CHIP_Center.pdf Proposal]
			[[Media:Evasive_Spike_Variants_Elucidate_the_Preservation_of_T_Cell_Immune_Response_to_the_SARS-CoV-2_Omicron_Variant.pdf \| Paper]]
	\|}		\|}

MarcRiedel: /* Computing with Molecules */

2024-02-07T21:26:01Z

Computing with Molecules

← Older revision		Revision as of 21:26, 7 February 2024
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	\|- valign="top"		\|- valign="top"
	\| '''~~to appear~~ in''':		\| '''appeared in''':
	\| [https://~~www~~.springer.com/~~journal~~/~~11047~~ Natural Computing], 2023		\| [https://link.springer.com/article/10.1007/s11047-023-09964-z Natural Computing], 2023
	\|- valign="top"		\|- valign="top"
	\| '''presented at''':		\| '''presented at''':

MarcRiedel: /* Storing Data with Molecules */

2024-02-07T21:22:44Z

Storing Data with Molecules

← Older revision		Revision as of 21:22, 7 February 2024
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	\|- valign="top"		\|- valign="top"
	\|'''appeared in''':		\|'''appeared in''':
	\|[https://pubs.rsc.org/en/content/articlepdf/2023/DD/D3DD00083D?page=search Royal Society of Chemistry – Digital Discovery], Vol. 2, pp. 1436--1451, 2023		\|[https://pubs.rsc.org/en/content/articlepdf/2023/DD/D3DD00083D?page=search Royal Society of Chemistry – Digital Discovery], Vol. 2, pp. 1436–1451, 2023
	\|}		\|}
	\| width="70" align="center" \|<span class="plainlinks"> [https://mriedel.ece.umn.edu/wiki/images/8/8f/Manicka_Stephan_Chari_Mendonsa_Okubo_Stolzberg-Schray_Reddy_Riedel_Automated_Routing_of_Droplets_for_DNA_Storage_on_a_Digital_Microfluidics_Platform.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>		\| width="70" align="center" \|<span class="plainlinks"> [https://mriedel.ece.umn.edu/wiki/images/8/8f/Manicka_Stephan_Chari_Mendonsa_Okubo_Stolzberg-Schray_Reddy_Riedel_Automated_Routing_of_Droplets_for_DNA_Storage_on_a_Digital_Microfluidics_Platform.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>

MarcRiedel: /* Storing Data with Molecules */

2024-02-07T21:22:20Z

Storing Data with Molecules

← Older revision		Revision as of 21:22, 7 February 2024
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	Peyton Okubo, John Stolzberg-Schray, Anil Reddy, and [http://mriedel.ece.umn.edu/wiki/index.php/Marc_Riedel Marc Riedel]		Peyton Okubo, John Stolzberg-Schray, Anil Reddy, and [http://mriedel.ece.umn.edu/wiki/index.php/Marc_Riedel Marc Riedel]
	\|- valign="top"		\|- valign="top"
	\|'''~~to appear~~ in''':		\|'''appeared in''':
	\|[https://pubs.rsc.org/en/content/articlepdf/2023/DD/D3DD00083D?page=search Royal Society of Chemistry – Digital Discovery], 2023		\|[https://pubs.rsc.org/en/content/articlepdf/2023/DD/D3DD00083D?page=search Royal Society of Chemistry – Digital Discovery], Vol. 2, pp. 1436--1451, 2023
	\|}		\|}
	\| width="70" align="center" \|<span class="plainlinks"> [https://mriedel.ece.umn.edu/wiki/images/8/8f/Manicka_Stephan_Chari_Mendonsa_Okubo_Stolzberg-Schray_Reddy_Riedel_Automated_Routing_of_Droplets_for_DNA_Storage_on_a_Digital_Microfluidics_Platform.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>		\| width="70" align="center" \|<span class="plainlinks"> [https://mriedel.ece.umn.edu/wiki/images/8/8f/Manicka_Stephan_Chari_Mendonsa_Okubo_Stolzberg-Schray_Reddy_Riedel_Automated_Routing_of_Droplets_for_DNA_Storage_on_a_Digital_Microfluidics_Platform.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>

MarcRiedel: /* Storing Data with Molecules */

2023-08-23T19:29:39Z

Storing Data with Molecules

← Older revision		Revision as of 19:29, 23 August 2023
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	Peyton Okubo, John Stolzberg-Schray, Anil Reddy, and [http://mriedel.ece.umn.edu/wiki/index.php/Marc_Riedel Marc Riedel]		Peyton Okubo, John Stolzberg-Schray, Anil Reddy, and [http://mriedel.ece.umn.edu/wiki/index.php/Marc_Riedel Marc Riedel]
	\|- valign="top"		\|- valign="top"
	\|'''~~under~~ ~~revision~~''':		\|'''to appear in''':
	\|[https://~~arxiv~~.org/~~abs~~/~~2211.15494~~ Royal Society of Chemistry – Digital Discovery], 2023		\|[https://pubs.rsc.org/en/content/articlepdf/2023/DD/D3DD00083D?page=search Royal Society of Chemistry – Digital Discovery], 2023
	\|}		\|}
	\| width="70" align="center" \|<span class="plainlinks"> [https://mriedel.ece.umn.edu/wiki/images/8/8f/Manicka_Stephan_Chari_Mendonsa_Okubo_Stolzberg-Schray_Reddy_Riedel_Automated_Routing_of_Droplets_for_DNA_Storage_on_a_Digital_Microfluidics_Platform.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>		\| width="70" align="center" \|<span class="plainlinks"> [https://mriedel.ece.umn.edu/wiki/images/8/8f/Manicka_Stephan_Chari_Mendonsa_Okubo_Stolzberg-Schray_Reddy_Riedel_Automated_Routing_of_Droplets_for_DNA_Storage_on_a_Digital_Microfluidics_Platform.pdf http://mriedel.ece.umn.edu/wiki/images/0/04/Pdf.jpg]</span>

MarcRiedel: /* Computing with Random Bit Streams */

2023-07-16T21:01:59Z

Computing with Random Bit Streams

← Older revision		Revision as of 21:01, 16 July 2023
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	'''<big>A Deterministic Approach</big>'''		'''<big>A Deterministic Approach</big>'''

	Having ~~pioneered~~ ~~the~~ ~~field~~ of ~~stochastic~~ ~~logic~~, we decided to reexamine its foundations. Why can complex functions be computed with such simple circuits when we compute on probabilities? Intuition might suggest that somehow we are harnessing deep aspects of probability theory. ''This intuition is <u>wrong</u>''.		Having championed stochastic logic for many years, we decided to reexamine its foundations. Why can complex functions be computed with such simple circuits when we compute on probabilities? Intuition might suggest that somehow we are harnessing deep aspects of probability theory. ''This intuition is <u>wrong</u>''.

	The keys is that we operate on uniform representation rather than a positional one. We showed that '''we can compute deterministically using the same structures that we use when computing stochastically.''' ''There is no need to do anything randomly!'' This upended the field that we had pioneered.		The keys is that we operate on uniform representation rather than a positional one. We showed that '''we can compute deterministically using the same structures that we use when computing stochastically.''' ''There is no need to do anything randomly!'' This upended the field that we had pioneered.

MarcRiedel: /* Computing with Molecules */

2023-07-16T15:53:29Z

Computing with Molecules

← Older revision		Revision as of 15:53, 16 July 2023
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	\|- valign="top"		\|- valign="top"
	\| '''~~under~~ ~~review~~ in''':		\| '''to appear in''':
	\| [https://www.springer.com/journal/11047 Natural Computing], 2023		\| [https://www.springer.com/journal/11047 Natural Computing], 2023
	\|- valign="top"		\|- valign="top"